From 415990f1e91179d24eaf9a649689028d9559be11 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 4 May 2026 14:41:57 -0600 Subject: [PATCH 01/43] fix floats being intepretted as strings on the CLI --- CHANGELOG.md | 6 ++++++ data/conda/meta.yaml | 2 +- nextflow.config | 6 +++--- subworkflows/abricate/tests/nextflow.config | 2 +- subworkflows/abritamr/tests/nextflow.config | 2 +- subworkflows/agrvate/tests/nextflow.config | 2 +- subworkflows/amrfinderplus/tests/nextflow.config | 2 +- subworkflows/ariba/tests/nextflow.config | 2 +- subworkflows/bactopia/assembler/tests/nextflow.config | 2 +- subworkflows/bactopia/qc/tests/nextflow.config | 2 +- subworkflows/bactopia/sketcher/tests/nextflow.config | 2 +- subworkflows/bakta/tests/nextflow.config | 2 +- subworkflows/blastn/tests/nextflow.config | 2 +- subworkflows/blastp/tests/nextflow.config | 2 +- subworkflows/blastx/tests/nextflow.config | 2 +- subworkflows/bracken/tests/nextflow.config | 2 +- subworkflows/btyper3/tests/nextflow.config | 2 +- subworkflows/busco/tests/nextflow.config | 2 +- subworkflows/checkm/tests/nextflow.config | 2 +- subworkflows/checkm2/tests/nextflow.config | 2 +- subworkflows/clermontyping/tests/nextflow.config | 2 +- subworkflows/clonalframeml/tests/nextflow.config | 2 +- subworkflows/defensefinder/tests/nextflow.config | 2 +- subworkflows/ectyper/tests/nextflow.config | 2 +- subworkflows/eggnog/tests/nextflow.config | 2 +- subworkflows/emmtyper/tests/nextflow.config | 2 +- subworkflows/fastani/tests/nextflow.config | 2 +- subworkflows/gamma/tests/nextflow.config | 2 +- subworkflows/genotyphi/tests/nextflow.config | 2 +- subworkflows/gigatyper/tests/nextflow.config | 2 +- subworkflows/gtdb/tests/nextflow.config | 2 +- subworkflows/gubbins/tests/nextflow.config | 2 +- subworkflows/hicap/tests/nextflow.config | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 2 +- subworkflows/iqtree/tests/nextflow.config | 2 +- subworkflows/ismapper/tests/nextflow.config | 2 +- subworkflows/kleborate/tests/nextflow.config | 2 +- subworkflows/kraken2/tests/nextflow.config | 2 +- subworkflows/legsta/tests/nextflow.config | 2 +- subworkflows/lissero/tests/nextflow.config | 2 +- subworkflows/mashdist/tests/nextflow.config | 2 +- subworkflows/mashtree/tests/nextflow.config | 2 +- subworkflows/mcroni/tests/nextflow.config | 2 +- subworkflows/meningotype/tests/nextflow.config | 2 +- subworkflows/merlin/tests/nextflow.config | 2 +- subworkflows/merlindist/tests/nextflow.config | 2 +- subworkflows/midas/tests/nextflow.config | 2 +- subworkflows/mlst/tests/nextflow.config | 2 +- subworkflows/mobsuite/tests/nextflow.config | 2 +- subworkflows/mykrobe/tests/nextflow.config | 2 +- subworkflows/ncbigenomedownload/tests/nextflow.config | 2 +- subworkflows/ngmaster/tests/nextflow.config | 2 +- subworkflows/nohuman/tests/nextflow.config | 2 +- subworkflows/panaroo/tests/nextflow.config | 2 +- subworkflows/pangenome/tests/nextflow.config | 2 +- subworkflows/pasty/tests/nextflow.config | 2 +- subworkflows/pbptyper/tests/nextflow.config | 2 +- subworkflows/phispy/tests/nextflow.config | 2 +- subworkflows/pirate/tests/nextflow.config | 2 +- subworkflows/plasmidfinder/tests/nextflow.config | 2 +- subworkflows/pneumocat/tests/nextflow.config | 2 +- subworkflows/prokka/tests/nextflow.config | 2 +- subworkflows/quast/tests/nextflow.config | 2 +- subworkflows/rgi/tests/nextflow.config | 2 +- subworkflows/roary/tests/nextflow.config | 2 +- subworkflows/sccmec/tests/nextflow.config | 2 +- subworkflows/scoary/tests/nextflow.config | 2 +- subworkflows/scrubber/tests/nextflow.config | 2 +- subworkflows/seqsero2/tests/nextflow.config | 2 +- subworkflows/seroba/tests/nextflow.config | 2 +- subworkflows/shigapass/tests/nextflow.config | 2 +- subworkflows/shigatyper/tests/nextflow.config | 2 +- subworkflows/shigeifinder/tests/nextflow.config | 2 +- subworkflows/sistr/tests/nextflow.config | 2 +- subworkflows/snippy/core/tests/nextflow.config | 2 +- subworkflows/snippy/run/tests/nextflow.config | 2 +- subworkflows/snpdists/tests/nextflow.config | 2 +- subworkflows/spatyper/tests/nextflow.config | 2 +- subworkflows/srahumanscrubber/tests/nextflow.config | 2 +- subworkflows/ssuissero/tests/nextflow.config | 2 +- subworkflows/staphopiasccmec/tests/nextflow.config | 2 +- subworkflows/staphtyper/tests/nextflow.config | 2 +- subworkflows/stecfinder/tests/nextflow.config | 2 +- subworkflows/sylph/tests/nextflow.config | 2 +- subworkflows/tblastn/tests/nextflow.config | 2 +- subworkflows/tblastx/tests/nextflow.config | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 2 +- subworkflows/teton/tests/nextflow.config | 2 +- workflows/bactopia-tools/abricate/nextflow.config | 6 +++--- workflows/bactopia-tools/abritamr/nextflow.config | 6 +++--- workflows/bactopia-tools/agrvate/nextflow.config | 6 +++--- workflows/bactopia-tools/amrfinderplus/nextflow.config | 6 +++--- workflows/bactopia-tools/ariba/nextflow.config | 6 +++--- workflows/bactopia-tools/bakta/nextflow.config | 6 +++--- workflows/bactopia-tools/blastn/nextflow.config | 6 +++--- workflows/bactopia-tools/blastp/nextflow.config | 6 +++--- workflows/bactopia-tools/blastx/nextflow.config | 6 +++--- workflows/bactopia-tools/bracken/nextflow.config | 6 +++--- workflows/bactopia-tools/btyper3/nextflow.config | 6 +++--- workflows/bactopia-tools/busco/nextflow.config | 6 +++--- workflows/bactopia-tools/checkm/nextflow.config | 6 +++--- workflows/bactopia-tools/checkm2/nextflow.config | 6 +++--- workflows/bactopia-tools/clermontyping/nextflow.config | 6 +++--- workflows/bactopia-tools/defensefinder/nextflow.config | 6 +++--- workflows/bactopia-tools/ectyper/nextflow.config | 6 +++--- workflows/bactopia-tools/eggnog/nextflow.config | 6 +++--- workflows/bactopia-tools/emmtyper/nextflow.config | 6 +++--- workflows/bactopia-tools/fastani/nextflow.config | 6 +++--- workflows/bactopia-tools/gamma/nextflow.config | 6 +++--- workflows/bactopia-tools/genotyphi/nextflow.config | 6 +++--- workflows/bactopia-tools/gigatyper/nextflow.config | 6 +++--- workflows/bactopia-tools/gtdb/nextflow.config | 6 +++--- workflows/bactopia-tools/hicap/nextflow.config | 6 +++--- workflows/bactopia-tools/hpsuissero/nextflow.config | 6 +++--- workflows/bactopia-tools/ismapper/nextflow.config | 6 +++--- workflows/bactopia-tools/kleborate/nextflow.config | 6 +++--- workflows/bactopia-tools/kraken2/nextflow.config | 6 +++--- workflows/bactopia-tools/legsta/nextflow.config | 6 +++--- workflows/bactopia-tools/lissero/nextflow.config | 6 +++--- workflows/bactopia-tools/mashdist/nextflow.config | 6 +++--- workflows/bactopia-tools/mashtree/nextflow.config | 6 +++--- workflows/bactopia-tools/mcroni/nextflow.config | 6 +++--- workflows/bactopia-tools/meningotype/nextflow.config | 6 +++--- workflows/bactopia-tools/merlin/nextflow.config | 6 +++--- workflows/bactopia-tools/midas/nextflow.config | 6 +++--- workflows/bactopia-tools/mlst/nextflow.config | 6 +++--- workflows/bactopia-tools/mobsuite/nextflow.config | 6 +++--- workflows/bactopia-tools/mykrobe/nextflow.config | 6 +++--- workflows/bactopia-tools/ngmaster/nextflow.config | 6 +++--- workflows/bactopia-tools/pangenome/nextflow.config | 6 +++--- workflows/bactopia-tools/pasty/nextflow.config | 6 +++--- workflows/bactopia-tools/pbptyper/nextflow.config | 6 +++--- workflows/bactopia-tools/phispy/nextflow.config | 6 +++--- workflows/bactopia-tools/plasmidfinder/nextflow.config | 6 +++--- workflows/bactopia-tools/pneumocat/nextflow.config | 6 +++--- workflows/bactopia-tools/prokka/nextflow.config | 6 +++--- workflows/bactopia-tools/quast/nextflow.config | 6 +++--- workflows/bactopia-tools/rgi/nextflow.config | 6 +++--- workflows/bactopia-tools/sccmec/nextflow.config | 6 +++--- workflows/bactopia-tools/scrubber/nextflow.config | 6 +++--- workflows/bactopia-tools/seqsero2/nextflow.config | 6 +++--- workflows/bactopia-tools/seroba/nextflow.config | 6 +++--- workflows/bactopia-tools/shigapass/nextflow.config | 6 +++--- workflows/bactopia-tools/shigatyper/nextflow.config | 6 +++--- workflows/bactopia-tools/shigeifinder/nextflow.config | 6 +++--- workflows/bactopia-tools/sistr/nextflow.config | 6 +++--- workflows/bactopia-tools/snippy/nextflow.config | 6 +++--- workflows/bactopia-tools/spatyper/nextflow.config | 6 +++--- workflows/bactopia-tools/ssuissero/nextflow.config | 6 +++--- workflows/bactopia-tools/staphtyper/nextflow.config | 6 +++--- workflows/bactopia-tools/stecfinder/nextflow.config | 6 +++--- workflows/bactopia-tools/sylph/nextflow.config | 6 +++--- workflows/bactopia-tools/tblastn/nextflow.config | 6 +++--- workflows/bactopia-tools/tblastx/nextflow.config | 6 +++--- workflows/bactopia-tools/tbprofiler/nextflow.config | 6 +++--- workflows/cleanyerreads/nextflow.config | 6 +++--- workflows/staphopia/nextflow.config | 6 +++--- workflows/teton/nextflow.config | 6 +++--- 158 files changed, 305 insertions(+), 299 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 00ca6ceee..9685f3e19 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,12 @@ sidebar_position: 5000 # Changelog +## v4.0.1 bactopia/bactopia "???" 2026/??/?? + +### `Fixed` + +- float parameters being interpreted as strings in CLI + ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 0af535e1a..ae1415469 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '4.0.0' %} +{% set version = '4.0.1' %} package: name: bactopia diff --git a/nextflow.config b/nextflow.config index fbb55d5b4..6a6ba157d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -118,7 +118,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index 0b3ce3cc2..a153c5e75 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index 2a9a3ab77..07f23b283 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index d5d1dce4d..f08b78776 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index 395685991..30cb79c21 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index 86efc8794..904463918 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index e07318408..8b488eeb9 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -67,5 +67,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index 853220898..8d2f0f071 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -73,5 +73,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index 7cd818360..04a452a95 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index 71d3d9506..7aa03cc5e 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index 68bc0f28a..429f70d78 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index e1dc5cb6e..5351e878b 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index 841fabf7c..8e4fc83d0 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index e080d94d2..d614882a1 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index 5e89054c2..ab5d3f91c 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index c4db5f68e..f10ddb8a8 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index e5332305b..31318f4e3 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index c725faa6d..ac6a24b0a 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index b127dba38..a8eda4c78 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index 785fcccc8..f35fd542d 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index faa12ff5e..44dc76248 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index f0439c881..6ebefc1ac 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index c1ee171a9..07381c8b5 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index bf51a5802..c04b150a2 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index 5863b98c8..ca612124c 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index 7fc6183d2..81db1e27c 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index b3d07fc56..745dd7c38 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index 801dce6a4..7be65ccd1 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index af89ab35b..98089906f 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index c863e8c48..718584db2 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index 3c0e28ec4..fa6c6b4b8 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index 88d1d8beb..a431a4508 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index bd648d6e1..332e6e2e5 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index b84c2ce06..5193c9dea 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index 18248573d..7cc65d928 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index f054a2279..dd861e525 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index e3aa9f973..ac40b3a67 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index a0125a434..0d098c436 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index 440b7cb90..c309d6320 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index 6e2696539..eaa0f7757 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index b2272b413..24591604c 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index b4609696f..c7256ec61 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index 5f1e849df..a29c41deb 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -63,5 +63,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index 46617f18d..73bd799c7 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index 9df718d07..3ef36f59a 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index 1d604e4c3..e3db439c3 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index 16a0d65d6..82c56c197 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index 451a95599..1a0b37a8d 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config index 9cda874af..8fcbdd409 100644 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ b/subworkflows/ncbigenomedownload/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index d79cb5fb2..7ac389916 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index 98c21cdf3..751248e97 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index 2b2c5706f..9084347fa 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index 74a4728b3..ac22736f3 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index eec4f6c00..20d4a8be1 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index 53c7bbe6a..d3cb1b464 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index 3623c73c4..f852de98c 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index 00b6ea0ff..c2313846e 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index 796f701a5..e4f52b07a 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index 86597966f..c34daaa89 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index bc3a922dc..8d15f83ef 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index ae879db4c..d32eaa8b1 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index 30f267901..fc9fc99f7 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index f551f4674..d5f48b74c 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 58d97b1be..355ba6fd2 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index e529e369f..40fad6ba6 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index a4f739e9b..f98440a39 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -44,5 +44,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index 118a2f158..bbee8b3c8 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 91bb0ea19..388790a38 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index 09216b315..984ec5b02 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index 384c44c5d..080c86925 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index d0ae8e0ee..092fd04be 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index fd7ee410c..3642d1f14 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index 50f97a2c5..5dad185c8 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -39,5 +39,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index 746334a74..905b2f879 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index 125078bbb..dff537bd7 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index 4b78174bd..d2a51b8ad 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index 98c0e97a1..66f68f855 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index 230885a5a..da66a03ae 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index f8782bcfa..770d4eb34 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 13d1016ea..1a1df9cad 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index e0f76c23d..473f08e47 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index 048901603..610b235c0 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index 7f163b904..ade267553 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index 8978c25ee..e3ab98887 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index 477b5bdf7..4c36cb712 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index fb1c18aaa..c702247e2 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -42,5 +42,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index b352b72a3..bbdc147a6 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 52f43f263..90b4022ff 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index c57c2c9ac..ef7c44271 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index 7450f678a..d51635316 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index 2d2aae657..f7f43fa63 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 3bcc83f95..353f3da7c 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index 34a05df62..f2981e0cf 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index e6efae22b..ad2348b78 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index bab6722f9..9c2665781 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index acb6912e0..2b59b69e2 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index bb6cff889..7384d9432 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index d9e817f35..dec7deba4 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index db8cd0d06..96f19af6e 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 10f3f8b09..e78635e5a 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index c449fee6d..1751bb3eb 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 40dbdadd1..811c553a3 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 49cfeb69b..639241884 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index 9df967072..68ed5709f 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index f214cccc0..1baf120ac 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index 3d09685ba..c5ab4c6c4 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index 64c6b9aee..83b574e7a 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index 15da5b77c..c7d0ff291 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index 1d83174e0..75b0ffca1 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index 718df8d4a..c821d723f 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index 3371173e6..31095e8f2 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index c95b960c7..03b318a02 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 780214622..851469f6f 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index 680492be6..c6db59943 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index 628a3846e..9f974cc24 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index a46dc3fee..9c45c8551 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index f6464ce63..54e6981fc 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index f4cf44885..3db5ec573 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 66ba5acd0..47efe1c09 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 5d585a0c4..87c99dd8a 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index a0c581d98..e4fa46252 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index 0d40e6e69..d6bed9fc2 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -110,7 +110,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index 3ab9e54a3..893360009 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index cedd3ce26..78e871510 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index 78566399f..a0a54da66 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index ba8257128..d870f666d 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 9ea61c23d..8b936ae7d 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index 7def7e46e..fe2473167 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index 4a9fc0d4d..f7b809288 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index ce39d0c4c..80faea541 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index 682020bd1..02c137117 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 22642b30c..3615de80f 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index bae5107dd..b499e7325 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index 4f09912fe..f9860a738 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index dee8a484d..703852180 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index 805bfd5ca..a653f0d88 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index 9ed7271ee..fa24a7a27 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index a80c9cef2..c2990e775 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index f215844cf..c7bbf9714 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index f240ae87a..d7d49c08b 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 2e432909b..8ed43d263 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 8e097cd86..5e6bb0cbf 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 9c8fdb657..d17d57d96 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index 4b22e4d4a..257777b05 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 6255206b7..c2447a210 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index fcde5236d..ee91c1b67 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 6f19835b8..0506e5405 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 0d654e02e..86179a3d3 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index aa4bd5ac3..b0a089473 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 73799fca9..67820ab5b 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index ed4ca8575..b38774b59 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 237ce8a62..31778291a 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 8062f4194..2ddc35a4f 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index 06cd5ea5d..206e0096d 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index e69011472..4f8600fac 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -97,7 +97,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 2fb367714..0ca83b75e 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -92,7 +92,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.2' } bactopia { From 21271b95d82663a9fb938c932ac6848a9df085a0 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 4 May 2026 20:17:12 -0600 Subject: [PATCH 02/43] fix scrubber when missing params, bump plugin version --- modules/srahumanscrubber/initdb/main.nf | 4 ++-- nextflow.config | 2 +- subworkflows/abricate/tests/nextflow.config | 2 +- subworkflows/abritamr/tests/nextflow.config | 2 +- subworkflows/agrvate/tests/nextflow.config | 2 +- subworkflows/amrfinderplus/tests/nextflow.config | 2 +- subworkflows/ariba/tests/nextflow.config | 2 +- subworkflows/bactopia/assembler/tests/nextflow.config | 2 +- subworkflows/bactopia/qc/tests/nextflow.config | 2 +- subworkflows/bactopia/sketcher/tests/nextflow.config | 2 +- subworkflows/bakta/tests/nextflow.config | 2 +- subworkflows/blastn/tests/nextflow.config | 2 +- subworkflows/blastp/tests/nextflow.config | 2 +- subworkflows/blastx/tests/nextflow.config | 2 +- subworkflows/bracken/tests/nextflow.config | 2 +- subworkflows/btyper3/tests/nextflow.config | 2 +- subworkflows/busco/tests/nextflow.config | 2 +- subworkflows/checkm/tests/nextflow.config | 2 +- subworkflows/checkm2/tests/nextflow.config | 2 +- subworkflows/clermontyping/tests/nextflow.config | 2 +- subworkflows/clonalframeml/tests/nextflow.config | 2 +- subworkflows/defensefinder/tests/nextflow.config | 2 +- subworkflows/ectyper/tests/nextflow.config | 2 +- subworkflows/eggnog/tests/nextflow.config | 2 +- subworkflows/emmtyper/tests/nextflow.config | 2 +- subworkflows/fastani/tests/nextflow.config | 2 +- subworkflows/gamma/tests/nextflow.config | 2 +- subworkflows/genotyphi/tests/nextflow.config | 2 +- subworkflows/gigatyper/tests/nextflow.config | 2 +- subworkflows/gtdb/tests/nextflow.config | 2 +- subworkflows/gubbins/tests/nextflow.config | 2 +- subworkflows/hicap/tests/nextflow.config | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 2 +- subworkflows/iqtree/tests/nextflow.config | 2 +- subworkflows/ismapper/tests/nextflow.config | 2 +- subworkflows/kleborate/tests/nextflow.config | 2 +- subworkflows/kraken2/tests/nextflow.config | 2 +- subworkflows/legsta/tests/nextflow.config | 2 +- subworkflows/lissero/tests/nextflow.config | 2 +- subworkflows/mashdist/tests/nextflow.config | 2 +- subworkflows/mashtree/tests/nextflow.config | 2 +- subworkflows/mcroni/tests/nextflow.config | 2 +- subworkflows/meningotype/tests/nextflow.config | 2 +- subworkflows/merlin/tests/nextflow.config | 2 +- subworkflows/merlindist/tests/nextflow.config | 2 +- subworkflows/midas/tests/nextflow.config | 2 +- subworkflows/mlst/tests/nextflow.config | 2 +- subworkflows/mobsuite/tests/nextflow.config | 2 +- subworkflows/mykrobe/tests/nextflow.config | 2 +- subworkflows/ncbigenomedownload/tests/nextflow.config | 2 +- subworkflows/ngmaster/tests/nextflow.config | 2 +- subworkflows/nohuman/tests/nextflow.config | 2 +- subworkflows/panaroo/tests/nextflow.config | 2 +- subworkflows/pangenome/tests/nextflow.config | 2 +- subworkflows/pasty/tests/nextflow.config | 2 +- subworkflows/pbptyper/tests/nextflow.config | 2 +- subworkflows/phispy/tests/nextflow.config | 2 +- subworkflows/pirate/tests/nextflow.config | 2 +- subworkflows/plasmidfinder/tests/nextflow.config | 2 +- subworkflows/pneumocat/tests/nextflow.config | 2 +- subworkflows/prokka/tests/nextflow.config | 2 +- subworkflows/quast/tests/nextflow.config | 2 +- subworkflows/rgi/tests/nextflow.config | 2 +- subworkflows/roary/tests/nextflow.config | 2 +- subworkflows/sccmec/tests/nextflow.config | 2 +- subworkflows/scoary/tests/nextflow.config | 2 +- subworkflows/scrubber/main.nf | 5 +++-- subworkflows/scrubber/tests/nextflow.config | 2 +- subworkflows/seqsero2/tests/nextflow.config | 2 +- subworkflows/seroba/tests/nextflow.config | 2 +- subworkflows/shigapass/tests/nextflow.config | 2 +- subworkflows/shigatyper/tests/nextflow.config | 2 +- subworkflows/shigeifinder/tests/nextflow.config | 2 +- subworkflows/sistr/tests/nextflow.config | 2 +- subworkflows/snippy/core/tests/nextflow.config | 2 +- subworkflows/snippy/run/tests/nextflow.config | 2 +- subworkflows/snpdists/tests/nextflow.config | 2 +- subworkflows/spatyper/tests/nextflow.config | 2 +- subworkflows/srahumanscrubber/tests/nextflow.config | 2 +- subworkflows/ssuissero/tests/nextflow.config | 2 +- subworkflows/staphopiasccmec/tests/nextflow.config | 2 +- subworkflows/staphtyper/tests/nextflow.config | 2 +- subworkflows/stecfinder/tests/nextflow.config | 2 +- subworkflows/sylph/tests/nextflow.config | 2 +- subworkflows/tblastn/tests/nextflow.config | 2 +- subworkflows/tblastx/tests/nextflow.config | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 2 +- subworkflows/teton/tests/nextflow.config | 2 +- workflows/bactopia-tools/abricate/nextflow.config | 2 +- workflows/bactopia-tools/abritamr/nextflow.config | 2 +- workflows/bactopia-tools/agrvate/nextflow.config | 2 +- workflows/bactopia-tools/amrfinderplus/nextflow.config | 2 +- workflows/bactopia-tools/ariba/nextflow.config | 2 +- workflows/bactopia-tools/bakta/nextflow.config | 2 +- workflows/bactopia-tools/blastn/nextflow.config | 2 +- workflows/bactopia-tools/blastp/nextflow.config | 2 +- workflows/bactopia-tools/blastx/nextflow.config | 2 +- workflows/bactopia-tools/bracken/nextflow.config | 2 +- workflows/bactopia-tools/btyper3/nextflow.config | 2 +- workflows/bactopia-tools/busco/nextflow.config | 2 +- workflows/bactopia-tools/checkm/nextflow.config | 2 +- workflows/bactopia-tools/checkm2/nextflow.config | 2 +- workflows/bactopia-tools/clermontyping/nextflow.config | 2 +- workflows/bactopia-tools/defensefinder/nextflow.config | 2 +- workflows/bactopia-tools/ectyper/nextflow.config | 2 +- workflows/bactopia-tools/eggnog/nextflow.config | 2 +- workflows/bactopia-tools/emmtyper/nextflow.config | 2 +- workflows/bactopia-tools/fastani/nextflow.config | 2 +- workflows/bactopia-tools/gamma/nextflow.config | 2 +- workflows/bactopia-tools/genotyphi/nextflow.config | 2 +- workflows/bactopia-tools/gigatyper/nextflow.config | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 2 +- workflows/bactopia-tools/hicap/nextflow.config | 2 +- workflows/bactopia-tools/hpsuissero/nextflow.config | 2 +- workflows/bactopia-tools/ismapper/nextflow.config | 2 +- workflows/bactopia-tools/kleborate/nextflow.config | 2 +- workflows/bactopia-tools/kraken2/nextflow.config | 2 +- workflows/bactopia-tools/legsta/nextflow.config | 2 +- workflows/bactopia-tools/lissero/nextflow.config | 2 +- workflows/bactopia-tools/mashdist/nextflow.config | 2 +- workflows/bactopia-tools/mashtree/nextflow.config | 2 +- workflows/bactopia-tools/mcroni/nextflow.config | 2 +- workflows/bactopia-tools/meningotype/nextflow.config | 2 +- workflows/bactopia-tools/merlin/nextflow.config | 2 +- workflows/bactopia-tools/midas/nextflow.config | 2 +- workflows/bactopia-tools/mlst/nextflow.config | 2 +- workflows/bactopia-tools/mobsuite/nextflow.config | 2 +- workflows/bactopia-tools/mykrobe/nextflow.config | 2 +- workflows/bactopia-tools/ngmaster/nextflow.config | 2 +- workflows/bactopia-tools/pangenome/nextflow.config | 2 +- workflows/bactopia-tools/pasty/nextflow.config | 2 +- workflows/bactopia-tools/pbptyper/nextflow.config | 2 +- workflows/bactopia-tools/phispy/nextflow.config | 2 +- workflows/bactopia-tools/plasmidfinder/nextflow.config | 2 +- workflows/bactopia-tools/pneumocat/nextflow.config | 2 +- workflows/bactopia-tools/prokka/nextflow.config | 2 +- workflows/bactopia-tools/quast/nextflow.config | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 2 +- workflows/bactopia-tools/sccmec/nextflow.config | 2 +- workflows/bactopia-tools/scrubber/nextflow.config | 2 +- workflows/bactopia-tools/scrubber/nextflow_schema.json | 2 +- workflows/bactopia-tools/seqsero2/nextflow.config | 2 +- workflows/bactopia-tools/seroba/nextflow.config | 2 +- workflows/bactopia-tools/shigapass/nextflow.config | 2 +- workflows/bactopia-tools/shigatyper/nextflow.config | 2 +- workflows/bactopia-tools/shigeifinder/nextflow.config | 2 +- workflows/bactopia-tools/sistr/nextflow.config | 2 +- workflows/bactopia-tools/snippy/nextflow.config | 2 +- workflows/bactopia-tools/spatyper/nextflow.config | 2 +- workflows/bactopia-tools/ssuissero/nextflow.config | 2 +- workflows/bactopia-tools/staphtyper/nextflow.config | 2 +- workflows/bactopia-tools/stecfinder/nextflow.config | 2 +- workflows/bactopia-tools/sylph/nextflow.config | 2 +- workflows/bactopia-tools/tblastn/nextflow.config | 2 +- workflows/bactopia-tools/tblastx/nextflow.config | 2 +- workflows/bactopia-tools/tbprofiler/nextflow.config | 2 +- workflows/cleanyerreads/nextflow.config | 2 +- workflows/staphopia/nextflow.config | 2 +- workflows/teton/nextflow.config | 2 +- 159 files changed, 162 insertions(+), 161 deletions(-) diff --git a/modules/srahumanscrubber/initdb/main.nf b/modules/srahumanscrubber/initdb/main.nf index 782a989c6..0655d55d3 100644 --- a/modules/srahumanscrubber/initdb/main.nf +++ b/modules/srahumanscrubber/initdb/main.nf @@ -27,7 +27,7 @@ process SRAHUMANSCRUBBER_INITDB { output: record( - db: files("${prefix}/*human_filter.db*"), + db: file("${prefix}/sra-human-filter.db"), logs: files("${prefix}/logs/*", optional: true) ) @@ -36,7 +36,7 @@ process SRAHUMANSCRUBBER_INITDB { """ mkdir -p ${prefix}/logs DBVERSION=\$(curl "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/current/version.txt") - curl -f "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/human_filter.db.\${DBVERSION}" -o "${prefix}/\${DBVERSION}.human_filter.db" + curl -f "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/human_filter.db.\${DBVERSION}" -o "${prefix}/sra-human-filter.db" # Move outputs to tool specific folder cp .command.begin ${prefix}/logs/nf.command.begin diff --git a/nextflow.config b/nextflow.config index 6a6ba157d..bf201ff01 100644 --- a/nextflow.config +++ b/nextflow.config @@ -118,7 +118,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index a153c5e75..db0fd5742 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index 07f23b283..2587a5739 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index f08b78776..34bd39493 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index 30cb79c21..8dcb5ea63 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index 904463918..da3bd4372 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index 8b488eeb9..b45f40e7f 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -67,5 +67,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index 8d2f0f071..3cd9d2448 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -73,5 +73,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index 04a452a95..9569170ae 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index 7aa03cc5e..3c244c8b1 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index 429f70d78..f46904a5f 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index 5351e878b..b127830ab 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index 8e4fc83d0..8ba4fd744 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index d614882a1..2faf2a18f 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index ab5d3f91c..90e0b1111 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index f10ddb8a8..0d6895014 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index 31318f4e3..b96ed6848 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index ac6a24b0a..c02336b5f 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index a8eda4c78..099da2304 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index f35fd542d..7a8726e64 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index 44dc76248..9b3140316 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index 6ebefc1ac..cdfe2f6f2 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index 07381c8b5..ac1e85693 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index c04b150a2..28bab2202 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index ca612124c..7993be709 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index 81db1e27c..40930c6d3 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index 745dd7c38..3f9ca61e2 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index 7be65ccd1..eec915931 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index 98089906f..6d703e73e 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index 718584db2..13aaaad7e 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index fa6c6b4b8..2613405f5 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index a431a4508..015e018db 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index 332e6e2e5..07cd5c506 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index 5193c9dea..5342b926b 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index 7cc65d928..884cae7cf 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index dd861e525..d8ac1e946 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index ac40b3a67..23152a892 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index 0d098c436..6376926b8 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index c309d6320..f9a07876f 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index eaa0f7757..74301eeb4 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index 24591604c..5ab5a616d 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index c7256ec61..a24fcfc35 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index a29c41deb..8d2de7898 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -63,5 +63,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index 73bd799c7..360d0e504 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index 3ef36f59a..b737504c2 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index e3db439c3..bff9533eb 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index 82c56c197..c72928095 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index 1a0b37a8d..d4a850f33 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config index 8fcbdd409..3dd7e2c5a 100644 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ b/subworkflows/ncbigenomedownload/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index 7ac389916..3ce246e5e 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index 751248e97..8f108cfc5 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index 9084347fa..0ca9317b2 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index ac22736f3..6599e1b0d 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index 20d4a8be1..50303b6b3 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index d3cb1b464..5443f0ef9 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index f852de98c..31d78636a 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index c2313846e..a74a1d24d 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index e4f52b07a..2dc14b1f9 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index c34daaa89..87296e133 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index 8d15f83ef..527cd1942 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index d32eaa8b1..b254fa002 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index fc9fc99f7..93fdfa3f7 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index d5f48b74c..4e06fdd9c 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 355ba6fd2..23bd5d921 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index 40fad6ba6..125183bf4 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/scrubber/main.nf b/subworkflows/scrubber/main.nf index 44a6168cb..6bbf88a15 100644 --- a/subworkflows/scrubber/main.nf +++ b/subworkflows/scrubber/main.nf @@ -80,13 +80,14 @@ workflow SCRUBBER { main: ch_sample_outputs = channel.empty() ch_special_report = channel.empty() + ch_reads = filterWithData(reads, ['r1', 'r2', 'se', 'lr']) if (use_srascrubber) { - ch_srahumanscrubber = SRAHUMANSCRUBBER(reads) + ch_srahumanscrubber = SRAHUMANSCRUBBER(ch_reads) ch_sample_outputs = ch_srahumanscrubber.sample_outputs ch_special_report = ch_srahumanscrubber.sample_outputs.map { r -> record(special_meta: r.special_meta, scrub_report: r.scrub_report) } } else { - ch_nohuman = NOHUMAN(reads, nohuman_db, download_nohuman, nohuman_save_as_tarball) + ch_nohuman = NOHUMAN(ch_reads, nohuman_db, download_nohuman, nohuman_save_as_tarball) ch_sample_outputs = ch_nohuman.sample_outputs ch_special_report = ch_nohuman.sample_outputs.map { r -> record(special_meta: r.special_meta, scrub_report: r.scrub_report) } } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index f98440a39..ef36d023a 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -44,5 +44,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index bbee8b3c8..6c2c44e66 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 388790a38..37b0c80b1 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index 984ec5b02..69c46dbca 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index 080c86925..bb5fade2b 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index 092fd04be..a7bdacb7f 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index 3642d1f14..4374b82bc 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index 5dad185c8..a26c906d1 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -39,5 +39,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index 905b2f879..89b6aa835 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index dff537bd7..f8cac4d81 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index d2a51b8ad..31f4358e1 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index 66f68f855..23232a696 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index da66a03ae..20e680383 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index 770d4eb34..4a5787e1c 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 1a1df9cad..4b65ac350 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index 473f08e47..973e89a45 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index 610b235c0..698ade699 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index ade267553..f60f3ced7 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index e3ab98887..69ee863c3 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index 4c36cb712..7685427ad 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index c702247e2..5a4a940a9 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -42,5 +42,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index bbdc147a6..386ab973c 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 90b4022ff..64fd11cbc 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index ef7c44271..59879e6c1 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index d51635316..21b141c2a 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index f7f43fa63..16a212fff 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 353f3da7c..407a7aa3a 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index f2981e0cf..c651544cd 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index ad2348b78..27d058f86 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 9c2665781..455b2c293 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 2b59b69e2..27abf0dfc 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index 7384d9432..0fe6e4b56 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index dec7deba4..88d5b1a72 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index 96f19af6e..d2284a32b 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index e78635e5a..953c7156a 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index 1751bb3eb..ad1821f2e 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 811c553a3..abeaffb5d 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 639241884..978a54aa0 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index 68ed5709f..d43289951 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index 1baf120ac..fed4f3bdc 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index c5ab4c6c4..da03ae80f 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index 83b574e7a..cffab56f3 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index c7d0ff291..5b9986635 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index 75b0ffca1..4cbbb75d6 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index c821d723f..39ca847c3 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index 31095e8f2..b882d16aa 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index 03b318a02..e5e6416d8 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 851469f6f..2244f1bab 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index c6db59943..fc86cab21 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index 9f974cc24..a745b1610 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 9c45c8551..0ac376101 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index 54e6981fc..50b367ed8 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index 3db5ec573..3b630fbf8 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 47efe1c09..05f14daee 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 87c99dd8a..11a4f1503 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index e4fa46252..db72912f1 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index d6bed9fc2..23eb3b288 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -110,7 +110,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index 893360009..cbf1a09fc 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index 78e871510..d1c338dfc 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index a0a54da66..75c39e24b 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index d870f666d..7f39a41bf 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 8b936ae7d..7f1b190fb 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index fe2473167..02d08b735 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index f7b809288..bd300c69d 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index 80faea541..6352ef33b 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index 02c137117..da2500034 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 3615de80f..9bd7be7ff 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index b499e7325..3c9d97f37 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index f9860a738..ee4c3c346 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 703852180..3109a2c19 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index a653f0d88..6c6caf404 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index fa24a7a27..6c2a99e82 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index c2990e775..ef541fd3e 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow_schema.json b/workflows/bactopia-tools/scrubber/nextflow_schema.json index 723ba7bc9..99b311223 100644 --- a/workflows/bactopia-tools/scrubber/nextflow_schema.json +++ b/workflows/bactopia-tools/scrubber/nextflow_schema.json @@ -516,4 +516,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} \ No newline at end of file +} diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index c7bbf9714..da3b5c530 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index d7d49c08b..26a32aa8e 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 8ed43d263..c81fa9a48 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 5e6bb0cbf..140815fda 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index d17d57d96..c12ea87d8 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index 257777b05..021712e8a 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index c2447a210..9d0564501 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index ee91c1b67..ff362ddef 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 0506e5405..51023c783 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 86179a3d3..38449328b 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index b0a089473..d9f181c98 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 67820ab5b..bbe1cb21e 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index b38774b59..1963b2c35 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 31778291a..e5591d523 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 2ddc35a4f..7e481d2ba 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index 206e0096d..48b90318e 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 4f8600fac..0a7eb6a99 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -97,7 +97,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 0ca83b75e..4f9f8bfdd 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -92,7 +92,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.2' + id 'nf-bactopia@2.1.3' } bactopia { From eed31964aa9f6205946cded3fd24232c6618d8f8 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 5 May 2026 12:12:37 -0600 Subject: [PATCH 03/43] add bactopia tool for staphscan --- .vscode/settings.json | 1 + catalog.json | 77 ++- data/citations.yml | 7 + llms.txt | 4 +- modules/staphscan/main.nf | 92 ++++ modules/staphscan/module.config | 25 + modules/staphscan/schema.json | 35 ++ modules/staphscan/tests/main.nf.test | 38 ++ modules/staphscan/tests/main.nf.test.snap | 23 + modules/staphscan/tests/nextflow.config | 36 ++ modules/staphscan/tests/nf-test.config | 11 + subworkflows/staphscan/main.nf | 49 ++ subworkflows/staphscan/tests/.nftignore | 2 + subworkflows/staphscan/tests/main.nf.test | 46 ++ .../staphscan/tests/main.nf.test.snap | 34 ++ subworkflows/staphscan/tests/nextflow.config | 40 ++ subworkflows/staphscan/tests/nf-test.config | 11 + workflows/bactopia-tools/staphscan/main.nf | 86 ++++ .../bactopia-tools/staphscan/nextflow.config | 91 ++++ .../staphscan/nextflow_schema.json | 453 ++++++++++++++++++ .../bactopia-tools/staphscan/tests/.nftignore | 3 + .../staphscan/tests/main.nf.test | 43 ++ .../staphscan/tests/main.nf.test.snap | 51 ++ .../staphscan/tests/nf-test.config | 11 + 24 files changed, 1263 insertions(+), 6 deletions(-) create mode 100644 modules/staphscan/main.nf create mode 100644 modules/staphscan/module.config create mode 100644 modules/staphscan/schema.json create mode 100644 modules/staphscan/tests/main.nf.test create mode 100644 modules/staphscan/tests/main.nf.test.snap create mode 100644 modules/staphscan/tests/nextflow.config create mode 100644 modules/staphscan/tests/nf-test.config create mode 100644 subworkflows/staphscan/main.nf create mode 100644 subworkflows/staphscan/tests/.nftignore create mode 100644 subworkflows/staphscan/tests/main.nf.test create mode 100644 subworkflows/staphscan/tests/main.nf.test.snap create mode 100644 subworkflows/staphscan/tests/nextflow.config create mode 100644 subworkflows/staphscan/tests/nf-test.config create mode 100644 workflows/bactopia-tools/staphscan/main.nf create mode 100644 workflows/bactopia-tools/staphscan/nextflow.config create mode 100644 workflows/bactopia-tools/staphscan/nextflow_schema.json create mode 100644 workflows/bactopia-tools/staphscan/tests/.nftignore create mode 100644 workflows/bactopia-tools/staphscan/tests/main.nf.test create mode 100644 workflows/bactopia-tools/staphscan/tests/main.nf.test.snap create mode 100644 workflows/bactopia-tools/staphscan/tests/nf-test.config diff --git a/.vscode/settings.json b/.vscode/settings.json index af2a622bd..ef4fefcc7 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -887,6 +887,7 @@ "Standley", "staphopia", "staphopiasccmec", + "staphscan", "staphtyper", "Starrett", "STEC", diff --git a/catalog.json b/catalog.json index 12fdbdcfb..42a58dcfc 100644 --- a/catalog.json +++ b/catalog.json @@ -1,9 +1,9 @@ { "version": "1.0", - "generated": "2026-04-29T11:30:57Z", - "bactopia_version": "4.0.0", - "bactopia_py_version": "2.1.2", - "nf_bactopia_version": "2.1.0", + "generated": "2026-05-05T18:04:27Z", + "bactopia_version": "4.0.1", + "bactopia_py_version": "2.1.6", + "nf_bactopia_version": "2.1.3", "modules": { "abricate_run": { "description": "Mass screening of contigs for antimicrobial and virulence genes.", @@ -2769,6 +2769,31 @@ ] } }, + "staphscan": { + "description": "Genome-based surveillance analysis of Staphylococcus aureus.", + "path": "modules/staphscan/", + "scope": "sample", + "process_name": "staphscan", + "tool": { + "name": "staphscan", + "version": "0.3.1" + }, + "takes": [ + "fna" + ], + "emits": [ + "tsv" + ], + "tags": { + "complexity": "simple", + "input_type": "single", + "output_type": "single", + "features": [ + "compression", + "conditional-logic" + ] + } + }, "stecfinder": { "description": "Serotype of Shigatoxin producing E. coli using reads/assemblies.", "path": "modules/stecfinder/", @@ -5883,6 +5908,39 @@ ] } }, + "staphscan": { + "description": "Genome-based surveillance analysis of Staphylococcus aureus.", + "path": "subworkflows/staphscan/", + "takes": [ + "fna" + ], + "takes_params": [ + "db" + ], + "emits": { + "sample_outputs": [ + "tsv" + ], + "run_outputs": [ + "csv" + ] + }, + "scope": "sample", + "calls": { + "modules": [ + "staphscan", + "csvtk_concat" + ] + }, + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "aggregation" + ] + } + }, "staphtyper": { "description": "Determine the agr, spa and SCCmec types for _Staphylococcus aureus_ genomes.", "path": "subworkflows/staphtyper/", @@ -6854,6 +6912,17 @@ "ssuissero" ] }, + "staphscan": { + "description": "Genome-based surveillance analysis of Staphylococcus aureus.", + "type": "tool", + "path": "workflows/bactopia-tools/staphscan/", + "ext": [ + "fna" + ], + "subworkflows": [ + "staphscan" + ] + }, "staphtyper": { "description": "Comprehensive typing of Staphylococcus aureus genomes.", "type": "tool", diff --git a/data/citations.yml b/data/citations.yml index c51eca1be..9ec1d3727 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -1038,6 +1038,13 @@ tools: cite: | Lui J [SsuisSero: Rapid _Streptococcus suis_ serotyping](https://github.com/jimmyliu1326/SsuisSero) (GitHub) + staphscan: + name: StaphSCAN + link: https://github.com/riccabolla/StaphSCAN + description: Genome-based surveillance analysis of _Staphylococcus aureus_ + cite: | + Bollini R [StaphSCAN (v0.3.0).](https://github.com/riccabolla/StaphSCAN) Zenodo (2026) + staphopiasccmec: name: staphopia-sccmec link: https://github.com/staphopia/staphopia-sccmec diff --git a/llms.txt b/llms.txt index 279a52351..69277502e 100644 --- a/llms.txt +++ b/llms.txt @@ -23,7 +23,7 @@ All components use standardized GroovyDoc documentation and static typing. - [workflows/cleanyerreads/](workflows/cleanyerreads/): Quality control and optional host read removal from raw sequencing reads. - [workflows/staphopia/](workflows/staphopia/): Comprehensive analysis pipeline for Staphylococcus aureus isolates. - [workflows/teton/](workflows/teton/): Taxonomic classification and abundance profiling of metagenomic reads. -- [workflows/bactopia-tools/](workflows/bactopia-tools/): 67 comparative analysis workflows (pan-genome, phylogenetics, typing) +- [workflows/bactopia-tools/](workflows/bactopia-tools/): 68 comparative analysis workflows (pan-genome, phylogenetics, typing) ## Subworkflows (Tier 2) @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -98 tool-specific modules live under `modules/`. Each module directory contains: +99 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/staphscan/main.nf b/modules/staphscan/main.nf new file mode 100644 index 000000000..3fefb284f --- /dev/null +++ b/modules/staphscan/main.nf @@ -0,0 +1,92 @@ +/** + * Genome-based surveillance analysis of Staphylococcus aureus. + * + * Uses [StaphSCAN](https://github.com/riccabolla/StaphSCAN) to perform genome-based + * surveillance of *Staphylococcus aureus*, integrating species identification, MLST, + * *spa* typing, SCCmec typing, capsular typing, and detection of virulence, biofilm, + * and antimicrobial resistance genes. + * + * @status stable + * @keywords staphylococcus aureus, surveillance, mlst, spa typing, sccmec, amr, virulence + * @tags complexity:simple input-type:single output-type:single features:compression,conditional-logic + * @citation staphscan + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @input db? + * Custom MLST database directory + * + * @output record(meta, tsv, results, logs, nf_logs, versions) + * - `tsv`: Per-sample surveillance summary with MLST, spa type, SCCmec, capsule, AGR, resistance, biofilm, and virulence results + */ +nextflow.enable.types = true + +process STAPHSCAN { + tag "${prefix}" + label 'process_low' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + record ( + meta: Record, + fna: Path + ) + db: Path? + + output: + record( + // Named fields (used downstream) + meta: meta, + tsv: file("${prefix}.tsv"), + // Generic fields (used for publishing) + results: [ + files("${prefix}.tsv") + ], + logs: files("*.{log,err}", optional: true), + nf_logs: files(".command.*"), + versions: files("versions.yml") + ) + + script: + def _meta = meta + prefix = task.ext.prefix ?: "${_meta.name}" + + // Create a new meta record + meta = record( + id: "${prefix}-${task.process}", + name: prefix, + scope: task.ext.scope, + output_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}", + logs_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}/logs/${task.ext.logs_subdir}", + process_name: task.ext.process_name + ) + + def is_compressed = fna.getName().endsWith(".gz") ? true : false + def fna_name = fna.getName().replace(".gz", "") + def db_args = db ? "--db_mlst ${db}" : "" + """ + if [ "${is_compressed}" == "true" ]; then + gzip -c -d ${fna} > ${fna_name} + fi + + staphscan \\ + -i ${fna_name} \\ + -o . \\ + --report ${prefix} \\ + ${db_args} ${task.ext.args} + + # Cleanup + if [ "${is_compressed}" == "true" ]; then + rm -rf ${fna_name} + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + staphscan: \$( staphscan --version 2>&1 | sed 's/^.*staphscan //' ) + END_VERSIONS + """ +} diff --git a/modules/staphscan/module.config b/modules/staphscan/module.config new file mode 100644 index 000000000..9d901351e --- /dev/null +++ b/modules/staphscan/module.config @@ -0,0 +1,25 @@ +params { + // staphscan + staphscan_modules = "" +} + +process { + withName: 'STAPHSCAN' { + ext.wf = params.wf + ext.scope = "sample" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "staphscan" + + // Tool arguments + ext.args = [ + params.staphscan_modules ? "--modules ${params.staphscan_modules}" : "", + ].join(' ').replaceAll("\\s{2,}", " ").trim() + + // Environment information + ext.toolName = "bioconda::staphscan=0.3.1".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/staphscan:0.3.1--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/staphscan:0.3.1--pyhdfd78af_0" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/staphscan/schema.json b/modules/staphscan/schema.json new file mode 100644 index 000000000..16642091e --- /dev/null +++ b/modules/staphscan/schema.json @@ -0,0 +1,35 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/staphscan/schema.json", + "title": "StaphSCAN Module", + "description": "A module for genome-based surveillance analysis of staphylococcus aureus", + "type": "object", + "$defs": { + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font" + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/staphscan_parameters" + } + ] +} diff --git a/modules/staphscan/tests/main.nf.test b/modules/staphscan/tests/main.nf.test new file mode 100644 index 000000000..50f6927b3 --- /dev/null +++ b/modules/staphscan/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + name "Test STAPHSCAN" + script "../main.nf" + process "STAPHSCAN" + tag "modules" + tag "staphscan" + + test("staphscan - module - GCF_000017085") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_000017085"], + fna: file("${params.test_data_dir}/species/staphylococcus_aureus/uncompressed/GCF_000017085/main/assembler/GCF_000017085.fna") + ) + ) + input[1] = null + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.tsv, + record.versions + ).match() } + ) + } + } +} diff --git a/modules/staphscan/tests/main.nf.test.snap b/modules/staphscan/tests/main.nf.test.snap new file mode 100644 index 000000000..65503ccd7 --- /dev/null +++ b/modules/staphscan/tests/main.nf.test.snap @@ -0,0 +1,23 @@ +{ + "staphscan - module - GCF_000017085": { + "content": [ + { + "id": "GCF_000017085-STAPHSCAN", + "logs_dir": "GCF_000017085/tools/staphscan//logs/", + "name": "GCF_000017085", + "output_dir": "GCF_000017085/tools/staphscan/", + "process_name": "staphscan", + "scope": "sample" + }, + "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + [ + "versions.yml:md5,466b4f78a712b55acb9520437caf3fea" + ] + ], + "timestamp": "2026-05-05T12:02:27.973597404", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/staphscan/tests/nextflow.config b/modules/staphscan/tests/nextflow.config new file mode 100644 index 000000000..91e332961 --- /dev/null +++ b/modules/staphscan/tests/nextflow.config @@ -0,0 +1,36 @@ +// Minimal config for module-level testing of STAPHSCAN +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "staphscan" + logo_name = "bactopia-tools" + description = "Genome-based surveillance analysis of Staphylococcus aureus" + ext = "fna" + } + + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +includeConfig "../module.config" +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" diff --git a/modules/staphscan/tests/nf-test.config b/modules/staphscan/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/modules/staphscan/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/subworkflows/staphscan/main.nf b/subworkflows/staphscan/main.nf new file mode 100644 index 000000000..131af8d70 --- /dev/null +++ b/subworkflows/staphscan/main.nf @@ -0,0 +1,49 @@ +/** + * Genome-based surveillance analysis of Staphylococcus aureus. + * + * This subworkflow uses [StaphSCAN](https://github.com/riccabolla/StaphSCAN) to perform + * genome-based surveillance of *Staphylococcus aureus*, integrating species identification, + * MLST, *spa* typing, SCCmec typing, capsular typing, and detection of virulence, biofilm, + * and antimicrobial resistance genes. It processes each sample individually and aggregates + * the results into a single consolidated report. + * + * @status stable + * @keywords staphylococcus aureus, surveillance, mlst, spa typing, sccmec, amr, virulence + * @tags complexity:moderate input-type:single output-type:multiple features:aggregation + * @citation staphscan + * + * @modules csvtk_concat, staphscan + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @input db + * Custom MLST database directory + * + * @output sample_outputs + * - `tsv`: Per-sample surveillance summary with MLST, spa type, SCCmec, capsule, AGR, resistance, biofilm, and virulence results + * + * @output run_outputs + * - `csv`: A merged TSV file with staphscan results from all samples + */ +nextflow.enable.types = true + +include { STAPHSCAN as STAPHSCAN_MODULE } from '../../modules/staphscan/main' +include { CSVTK_CONCAT } from '../../modules/csvtk/concat/main' +include { gatherCsvtk } from 'plugin/nf-bactopia' + +workflow STAPHSCAN { + take: + fna: Channel + db: Path? + + main: + ch_staphscan = STAPHSCAN_MODULE(fna, db) + ch_csvtk_concat = CSVTK_CONCAT(gatherCsvtk(ch_staphscan, 'tsv', [name: 'staphscan']), 'tsv', 'tsv') + + emit: + // Published outputs + sample_outputs = ch_staphscan + run_outputs = ch_csvtk_concat +} diff --git a/subworkflows/staphscan/tests/.nftignore b/subworkflows/staphscan/tests/.nftignore new file mode 100644 index 000000000..7b276dee3 --- /dev/null +++ b/subworkflows/staphscan/tests/.nftignore @@ -0,0 +1,2 @@ +**/*.{err,log,stderr,stdout} +**/*.command.* diff --git a/subworkflows/staphscan/tests/main.nf.test b/subworkflows/staphscan/tests/main.nf.test new file mode 100644 index 000000000..29f3f4873 --- /dev/null +++ b/subworkflows/staphscan/tests/main.nf.test @@ -0,0 +1,46 @@ +nextflow_workflow { + name "Test STAPHSCAN Subworkflow" + script "../main.nf" + workflow "STAPHSCAN" + tag "subworkflows" + tag "staphscan" + + test("staphscan - subworkflow - GCF_000017085") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_000017085"], + fna: file("${params.test_data_dir}/species/staphylococcus_aureus/compressed/GCF_000017085/main/assembler/GCF_000017085.fna.gz") + ) + ) + input[1] = null + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def run = workflow.out.run_outputs[0] + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs != null }, + { assert workflow.out.run_outputs != null }, + { assert snapshot( + sample.meta, + sample.tsv, + sample.versions, + run.meta, + run.versions + ).match() }, + { assert sample.results != null }, + { assert run.csv != null }, + { assert run.results != null } + ) + } + } +} diff --git a/subworkflows/staphscan/tests/main.nf.test.snap b/subworkflows/staphscan/tests/main.nf.test.snap new file mode 100644 index 000000000..55c91a903 --- /dev/null +++ b/subworkflows/staphscan/tests/main.nf.test.snap @@ -0,0 +1,34 @@ +{ + "staphscan - subworkflow - GCF_000017085": { + "content": [ + { + "id": "GCF_000017085-STAPHSCAN:STAPHSCAN_MODULE", + "logs_dir": "GCF_000017085/tools/staphscan//logs/", + "name": "GCF_000017085", + "output_dir": "GCF_000017085/tools/staphscan/", + "process_name": "staphscan", + "scope": "sample" + }, + "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + [ + "versions.yml:md5,21366a5b932268b20a58c129bf66d90b" + ], + { + "id": "staphscan-STAPHSCAN:CSVTK_CONCAT", + "logs_dir": "merged-results/logs/staphscan-concat/", + "name": "staphscan", + "output_dir": "merged-results", + "process_name": "staphscan-concat", + "scope": "run" + }, + [ + "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b" + ] + ], + "timestamp": "2026-05-05T12:03:39.31515092", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/staphscan/tests/nextflow.config b/subworkflows/staphscan/tests/nextflow.config new file mode 100644 index 000000000..bc566e5c0 --- /dev/null +++ b/subworkflows/staphscan/tests/nextflow.config @@ -0,0 +1,40 @@ +// Minimal config for subworkflow-level testing of STAPHSCAN +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "staphscan" + logo_name = "bactopia-tools" + description = "Genome-based surveillance analysis of Staphylococcus aureus" + ext = "fna" + } + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Load module configs for processes in this subworkflow +includeConfig "../../../modules/staphscan/module.config" +includeConfig "../../../modules/csvtk/concat/module.config" + +// Base config (container resolution + resource labels) +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" + +// Plugin +plugins { + id 'nf-bactopia@2.1.3' +} diff --git a/subworkflows/staphscan/tests/nf-test.config b/subworkflows/staphscan/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/subworkflows/staphscan/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/workflows/bactopia-tools/staphscan/main.nf b/workflows/bactopia-tools/staphscan/main.nf new file mode 100644 index 000000000..40a06ee6d --- /dev/null +++ b/workflows/bactopia-tools/staphscan/main.nf @@ -0,0 +1,86 @@ +#!/usr/bin/env nextflow +/** + * Genome-based surveillance analysis of Staphylococcus aureus. + * + * This Bactopia Tool uses [StaphSCAN](https://github.com/riccabolla/StaphSCAN) to perform + * genome-based surveillance of _Staphylococcus aureus_ for epidemiological typing and + * resistance profiling. + * + * @status stable + * @keywords staphylococcus aureus, surveillance, mlst, spa typing, sccmec, amr, virulence, bactopia-tool + * @tags complexity:simple input-type:parameter output-type:multiple features:bactopia-tool,aggregation + * @citation csvtk, staphscan + * + * @subworkflows utils_bactopia-tools, staphscan + * + * @input rundir + * Directory containing results from a completed Bactopia analysis run + * + * @input staphscan_db_mlst + * Path or tarball to custom MLST database (optional) + * + * @section Per-Sample Results + * @publish *.tsv Per-sample surveillance summary with MLST, spa type, SCCmec, capsule, AGR, resistance, biofilm, and virulence results + * + * @section Merged Results + * @publish staphscan.tsv Merged TSV file containing staphscan results from all samples + * + * @section Execution Logs + * @publish logs/staphscan/* Tool execution logs (stdout/stderr) + * @publish logs/nf-* Nextflow execution scripts and logs for debugging + * + * @section Versions + * @publish versions.yml Software version information + */ +nextflow.enable.types = true + +params { + rundir : String + + // Tool-specific parameters + staphscan_db_mlst : Path? +} + +include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' +include { STAPHSCAN } from '../../../subworkflows/staphscan/main' +include { collectNextflowLogs } from 'plugin/nf-bactopia' + +workflow { + main: + ch_bactopiatool = BACTOPIATOOL_INIT() + ch_staphscan = STAPHSCAN(ch_bactopiatool.assembly, params.staphscan_db_mlst) + + publish: + // Per-sample + sample_outputs = ch_staphscan.sample_outputs + sample_nf_logs = collectNextflowLogs(ch_staphscan.sample_outputs) + // Run-level + run_outputs = ch_staphscan.run_outputs + run_nf_logs = collectNextflowLogs(ch_staphscan.run_outputs) +} + +output { + // Sample-level outputs (stored in ${params.outdir}//) + sample_outputs { + path { r -> + r.results.flatten() >> "${r.meta.output_dir}/" + r.logs.flatten() >> "${r.meta.logs_dir}/" + r.versions.flatten() >> "${r.meta.logs_dir}/" + } + } + sample_nf_logs { + path { meta, f -> f >> "${meta.logs_dir}/nf${f.name}" } + } + + // Run-level outputs (stored in ${params.outdir}/bactopia-runs//) + run_outputs { + path { r -> + r.results.flatten() >> "${params.rundir}/${r.meta.output_dir}/" + r.logs.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + r.versions.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + } + } + run_nf_logs { + path { meta, f -> f >> "${params.rundir}/${meta.logs_dir}/nf${f.name}" } + } +} diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config new file mode 100644 index 000000000..1b2b14e18 --- /dev/null +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -0,0 +1,91 @@ +// main script name +manifest { + author = 'Robert A. Petit III' + name = 'bactopia' + homePage = 'https://github.com/bactopia/bactopia' + description = 'An extensive workflow for processing sequencing of bacterial genomes.' + mainScript = 'main.nf' + version = '4.0.1' + nextflowVersion = '>=26.04.0' +} + +params { + workflow { + name = "staphscan" + logo_name = "bactopia-tools" + description = "Genome-based surveillance analysis of Staphylococcus aureus." + ext = ['fna'] + } +} + +// Version +params.bactopia_version = '4.0.0' +manifest.version = "${params.bactopia_version}" + +// Includes +params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +includeConfig "../../../conf/params.config" +includeConfig "../../../conf/params/bactopia-tools.config" + +// Module specific config +includeConfig "../../../modules/csvtk/concat/module.config" +includeConfig "../../../modules/staphscan/module.config" + +// Set output directory +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode +workflow.output.overwrite = params.force + +// Set up run directory +params.singularity_cache = env("NXF_SINGULARITY_CACHEDIR") ? "${env('NXF_SINGULARITY_CACHEDIR')}" : "${params.singularity_cache}" +params.run_timestamp = new java.util.Date().format('yyyyMMdd-HHmmss') +params.rundir = params.is_ci ? "bactopia-runs/${params.run_name}" : "bactopia-runs/${params.run_name}-${params.run_timestamp}" +params.infodir = "${params.outdir}/${params.rundir}/nf-reports" + +// Load nf-core custom profiles from different Institutions +includeConfig !env('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + +// Load Bactopia custom profiles from different institutions. +// Uncomment in the event a bactopia specific profile is added +//includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bactopia.config" : "/dev/null" + +// Base Config +includeConfig "../../../conf/base.config" + +// Profiles +includeConfig "../../../conf/profiles.config" + +// Reporting configuration +timeline { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-timeline.html" +} + +report { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-report.html" +} + +trace { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-trace.txt" + fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem' +} + +dag { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-dag.svg" +} + +// Plugins +plugins { + id 'nf-bactopia@2.1.3' +} + +bactopia { + parametersSchema = "${projectDir}/nextflow_schema.json" +} diff --git a/workflows/bactopia-tools/staphscan/nextflow_schema.json b/workflows/bactopia-tools/staphscan/nextflow_schema.json new file mode 100644 index 000000000..330d1748a --- /dev/null +++ b/workflows/bactopia-tools/staphscan/nextflow_schema.json @@ -0,0 +1,453 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/bactopia-tools.json", + "title": "staphscan", + "description": "Genome-based surveillance analysis of Staphylococcus aureus.", + "type": "object", + "$defs": { + "input_parameters": { + "title": "Required Parameters", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "help_text": "", + "properties": { + "bactopia": { + "type": "string", + "description": "The path to bactopia results to use as inputs", + "help": "The required inputs will be automatically selected by the subworkflow.", + "fa_icon": "fas fa-bacterium", + "header": "Bactopia Results" + } + } + }, + "filter_parameters": { + "title": "Filtering Parameters", + "type": "object", + "description": "Use these parameters to specify which samples to include or exclude.", + "default": "", + "fa_icon": "fa-solid fa-filter", + "properties": { + "include": { + "type": "string", + "description": "A text file containing sample names (one per line) to include from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-plus" + }, + "exclude": { + "type": "string", + "description": "A text file containing sample names (one per line) to exclude from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-minus" + } + } + }, + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font" + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, + "csvtk_concat_parameters": { + "title": "csvtk concat Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "csvtk_concat_opts": { + "type": "string", + "description": "Extra csvtk concat options in quotes", + "help": "", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, + "optional_parameters": { + "title": "Optional Parameters", + "type": "object", + "description": "These optional parameters can be useful in certain settings.", + "default": "", + "fa_icon": "fa-solid fa-gears", + "properties": { + "outdir": { + "type": "string", + "default": "bactopia", + "description": "Base directory to write results to", + "fa_icon": "fas fa-folder" + }, + "skip_compression": { + "type": "boolean", + "default": false, + "description": "Output files will not be compressed", + "help": "Using this parameter can lead to a significant increase in the size of the outputs", + "fa_icon": "fas fa-expand-arrows-alt", + "hidden": true + }, + "datasets": { + "type": "string", + "fa_icon": "fas fa-folder", + "description": "The path to cache datasets to", + "hidden": true + }, + "keep_all_files": { + "type": "boolean", + "default": false, + "description": "Keeps all analysis files created", + "help": "By default, intermediate files are removed. This will not affect the ability to resume Nextflow runs, and only occurs at the end of the process.", + "fa_icon": "fas fa-trash-restore", + "hidden": true + } + } + }, + "max_job_request_parameters": { + "title": "Max Job Request Parameters", + "type": "object", + "fa_icon": "fa-solid fa-arrow-up-right-dots", + "description": "Set the top limit for requested resources for any single job.", + "hidden": true, + "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", + "properties": { + "max_retry": { + "type": "integer", + "description": "Maximum times to retry a process before allowing it to fail.", + "default": 3, + "fa_icon": "fas fa-redo", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of retry attempts for each process. Should be an integer e.g. `--max_retry 1`" + }, + "max_cpus": { + "type": "integer", + "description": "Maximum number of CPUs that can be requested for any single job.", + "default": 4, + "fa_icon": "fas fa-microchip", + "hidden": true, + "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" + }, + "max_memory": { + "type": "string", + "description": "Maximum amount of memory that can be requested for any single job.", + "default": "128.GB", + "fa_icon": "fas fa-memory", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "hidden": true, + "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" + }, + "max_time": { + "type": "string", + "description": "Maximum amount of time that can be requested for any single job.", + "default": "240.h", + "fa_icon": "far fa-clock", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", + "hidden": true, + "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '1.h'`" + }, + "max_downloads": { + "type": "integer", + "description": "Maximum number of samples to download at a time", + "default": 3, + "fa_icon": "fas fa-angle-double-up", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of downloads at a time" + } + } + }, + "nextflow_parameters": { + "title": "Nextflow Configuration Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-solid fa-screwdriver-wrench", + "properties": { + "nfconfig": { + "type": "string", + "description": "A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.", + "help": "This allows you to create profiles specific to your environment (e.g. SGE, AWS, SLURM, etc...).", + "fa_icon": "fas fa-cog", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "hidden": true, + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ] + }, + "infodir": { + "type": "string", + "description": "Directory to keep pipeline Nextflow logs and reports.", + "default": "${params.outdir}/pipeline_info", + "fa_icon": "fas fa-cogs", + "hidden": true + }, + "force": { + "type": "boolean", + "default": false, + "description": "Nextflow will overwrite existing output files.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "cleanup_workdir": { + "type": "boolean", + "default": false, + "description": "After Bactopia is successfully executed, the `work` directory will be deleted.", + "help": "Warning: by doing this you lose the ability to resume workflows.", + "fa_icon": "fas fa-trash-alt", + "hidden": true + } + } + }, + "institutional_config_options": { + "title": "Institutional config options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralized config profiles. These should not be edited.", + "help_text": "The centralized nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "properties": { + "custom_config_version": { + "type": "string", + "description": "Git commit id for Institutional configs.", + "default": "master", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "custom_config_base": { + "type": "string", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", + "hidden": true, + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" + }, + "config_profile_name": { + "type": "string", + "description": "Institutional config name.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_description": { + "type": "string", + "description": "Institutional config description.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_url": { + "type": "string", + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + } + } + }, + "nextflow_profile_parameters": { + "title": "Nextflow Profile Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-regular fa-address-card", + "properties": { + "condadir": { + "type": "string", + "description": "Directory to Nextflow should use for Conda environments", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "registry": { + "type": "string", + "default": "quay.io", + "hidden": true, + "description": "Registry to pull Docker containers from.", + "fa_icon": "fas fa-box" + }, + "datasets_cache": { + "type": "string", + "default": "/.bactopia/datasets", + "description": "Directory where downloaded datasets should be stored.", + "help": "", + "fa_icon": "fas fa-folder" + }, + "singularity_cache": { + "type": "string", + "description": "Directory where remote Singularity images are stored.", + "help": "If using a cluster, it must be accessible from all compute nodes. The NXF_SINGULARITY_CACHEDIR environment variable overrides this parameter", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.", + "hidden": true, + "fa_icon": "fas fa-toolbox", + "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues." + }, + "force_rebuild": { + "type": "boolean", + "default": false, + "description": "Force overwrite of existing pre-built environments.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "queue": { + "type": "string", + "default": "general,high-memory", + "description": "Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "cluster_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "container_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D `pwd`'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "disable_scratch": { + "type": "boolean", + "default": false, + "description": "All intermediate files created on worker nodes of will be transferred to the head node.", + "help": "Typically with clusters intermediate results are written to a 'scratch' space and only published result files are transferred back", + "fa_icon": "fas fa-toggle-off", + "hidden": true + } + } + }, + "generic_parameters": { + "title": "Helpful Parameters", + "type": "object", + "fa_icon": "fa-solid fa-reply-all", + "description": "Uncommonly used parameters that might be useful.", + "properties": { + "monochrome_logs": { + "type": "boolean", + "description": "Do not use coloured log outputs.", + "fa_icon": "fas fa-palette", + "hidden": true, + "help_text": "Set to disable colourful command line output and live life in monochrome." + }, + "nfdir": { + "type": "boolean", + "description": "Print directory Nextflow has pulled Bactopia to", + "fa_icon": "fas fa-remove-format", + "hidden": true + }, + "sleep_time": { + "type": "integer", + "description": "The amount of time (seconds) Nextflow will wait after setting up datasets before execution.", + "default": 5, + "fa_icon": "far fa-clock", + "hidden": true + }, + "validate_params": { + "type": "boolean", + "default": true, + "fa_icon": "fas fa-tasks", + "description": "Boolean whether to validate parameters against the schema at runtime", + "hidden": true + }, + "help": { + "type": "boolean", + "description": "Display help text.", + "hidden": true, + "fa_icon": "fas fa-question-circle" + }, + "wf": { + "type": "string", + "description": "Specify which workflow or Bactopia Tool to execute", + "default": "bactopia", + "fa_icon": "fas fa-bacteria" + }, + "list_wfs": { + "type": "boolean", + "description": "List the available workflows and Bactopia Tools to use with '--wf'", + "fa_icon": "fas fa-list" + }, + "show_hidden_params": { + "type": "boolean", + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters.", + "description": "Show all params when using `--help`", + "fa_icon": "far fa-eye", + "hidden": true + }, + "help_all": { + "type": "boolean", + "description": "An alias for --help --show_hidden_params", + "fa_icon": "fas fa-question-circle" + }, + "version": { + "type": "boolean", + "description": "Display version text.", + "fa_icon": "fas fa-info" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_parameters" + }, + { + "$ref": "#/$defs/filter_parameters" + }, + { + "$ref": "#/$defs/staphscan_parameters" + }, + { + "$ref": "#/$defs/csvtk_concat_parameters" + }, + { + "$ref": "#/$defs/optional_parameters" + }, + { + "$ref": "#/$defs/max_job_request_parameters" + }, + { + "$ref": "#/$defs/nextflow_parameters" + }, + { + "$ref": "#/$defs/nextflow_profile_parameters" + }, + { + "$ref": "#/$defs/generic_parameters" + } + ] +} \ No newline at end of file diff --git a/workflows/bactopia-tools/staphscan/tests/.nftignore b/workflows/bactopia-tools/staphscan/tests/.nftignore new file mode 100644 index 000000000..72a5fcb38 --- /dev/null +++ b/workflows/bactopia-tools/staphscan/tests/.nftignore @@ -0,0 +1,3 @@ +**/*.{err,gz,html,log,pdf,stderr,stdout} +**/nf.command.* +bactopia-runs/**/nf-reports/*.{dot,html} diff --git a/workflows/bactopia-tools/staphscan/tests/main.nf.test b/workflows/bactopia-tools/staphscan/tests/main.nf.test new file mode 100644 index 000000000..b3e2e5b71 --- /dev/null +++ b/workflows/bactopia-tools/staphscan/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_pipeline { + name "Test staphscan Workflow" + script "../main.nf" + config "../../../../conf/test.config" + tag "workflows" + tag "bactopia-tools" + tag "staphscan" + + test("staphscan - GCF_000017085|staphylococcus_aureus|compressed_fasta") { + when { + params { + bactopia_test = "/species/staphylococcus_aureus/compressed" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap new file mode 100644 index 000000000..2ea85b322 --- /dev/null +++ b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap @@ -0,0 +1,51 @@ +{ + "staphscan - GCF_000017085|staphylococcus_aureus|compressed_fasta": { + "content": [ + 2, + [ + "GCF_000017085", + "GCF_000017085/tools", + "GCF_000017085/tools/staphscan", + "GCF_000017085/tools/staphscan/GCF_000017085.tsv", + "GCF_000017085/tools/staphscan/logs", + "GCF_000017085/tools/staphscan/logs/nf.command.begin", + "GCF_000017085/tools/staphscan/logs/nf.command.err", + "GCF_000017085/tools/staphscan/logs/nf.command.log", + "GCF_000017085/tools/staphscan/logs/nf.command.out", + "GCF_000017085/tools/staphscan/logs/nf.command.run", + "GCF_000017085/tools/staphscan/logs/nf.command.sh", + "GCF_000017085/tools/staphscan/logs/nf.command.trace", + "GCF_000017085/tools/staphscan/logs/versions.yml", + "bactopia-runs", + "bactopia-runs/staphscan", + "bactopia-runs/staphscan/merged-results", + "bactopia-runs/staphscan/merged-results/logs", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.begin", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.err", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.log", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.out", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.run", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.sh", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/nf.command.trace", + "bactopia-runs/staphscan/merged-results/logs/staphscan-concat/versions.yml", + "bactopia-runs/staphscan/merged-results/staphscan.tsv", + "bactopia-runs/staphscan/nf-reports", + "bactopia-runs/staphscan/nf-reports/staphscan-dag.dot", + "bactopia-runs/staphscan/nf-reports/staphscan-report.html", + "bactopia-runs/staphscan/nf-reports/staphscan-timeline.html" + ], + [ + "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + "versions.yml:md5,21366a5b932268b20a58c129bf66d90b", + "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b", + "staphscan.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb" + ] + ], + "timestamp": "2026-05-05T12:05:58.045626143", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/workflows/bactopia-tools/staphscan/tests/nf-test.config b/workflows/bactopia-tools/staphscan/tests/nf-test.config new file mode 100644 index 000000000..8f297479d --- /dev/null +++ b/workflows/bactopia-tools/staphscan/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "../nextflow.config" + profile "" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} From cfed649e5cf6affec70e003a906937b1b81ea7d6 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 5 May 2026 13:38:50 -0600 Subject: [PATCH 04/43] add staphscan to staphtyper and merlin --- catalog.json | 13 +++++--- subworkflows/merlin/main.nf | 10 ++++-- subworkflows/staphtyper/main.nf | 33 ++++++++++++------- workflows/bactopia-tools/merlin/main.nf | 8 ++++- .../bactopia-tools/merlin/nextflow.config | 9 ++--- .../merlin/nextflow_schema.json | 24 ++++++++++++++ .../merlin/tests/main.nf.test.snap | 27 +++++++++++++-- workflows/bactopia-tools/staphtyper/main.nf | 12 +++++-- .../bactopia-tools/staphtyper/nextflow.config | 9 ++--- .../staphtyper/nextflow_schema.json | 24 ++++++++++++++ .../staphtyper/tests/main.nf.test.snap | 31 +++++++++++++++-- workflows/staphopia/main.nf | 10 ++++-- workflows/staphopia/nextflow.config | 9 ++--- workflows/staphopia/nextflow_schema.json | 26 +++++++++++++++ workflows/staphopia/tests/main.nf.test.snap | 29 ++++++++++++++-- 15 files changed, 227 insertions(+), 47 deletions(-) diff --git a/catalog.json b/catalog.json index 42a58dcfc..baaebeade 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-05-05T18:04:27Z", + "generated": "2026-05-05T19:22:52Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.1.6", "nf_bactopia_version": "2.1.3", @@ -4509,7 +4509,8 @@ "hicap_database_dir", "hicap_model_fp", "staphtyper_repeats", - "staphtyper_repeat_order" + "staphtyper_repeat_order", + "staphscan_db_mlst" ], "emits": { "sample_outputs": [], @@ -5942,14 +5943,15 @@ } }, "staphtyper": { - "description": "Determine the agr, spa and SCCmec types for _Staphylococcus aureus_ genomes.", + "description": "Determine the agr, spa, SCCmec types and perform genome-based surveillance for _Staphylococcus aureus_ genomes.", "path": "subworkflows/staphtyper/", "takes": [ "assembly" ], "takes_params": [ "repeats", - "repeat_order" + "repeat_order", + "staphscan_db_mlst" ], "emits": { "sample_outputs": [], @@ -5962,7 +5964,8 @@ "subworkflows": [ "agrvate", "spatyper", - "sccmec" + "sccmec", + "staphscan" ] }, "tags": { diff --git a/subworkflows/merlin/main.nf b/subworkflows/merlin/main.nf index c4ae1cf36..d16a87275 100644 --- a/subworkflows/merlin/main.nf +++ b/subworkflows/merlin/main.nf @@ -12,8 +12,8 @@ * @tags complexity:complex input-type:single output-type:multiple features:conditional-logic,components * @citation mash * - * @subworkflows merlindist, clermontyping, ectyper, emmtyper, genotyphi, hicap, hpsuissero, kleborate, - * legsta, lissero, ngmaster, pasty, pbptyper, seqsero2, seroba, shigapass, + * @subworkflows clermontyping, ectyper, emmtyper, genotyphi, hicap, hpsuissero, kleborate, + * legsta, lissero, merlindist, ngmaster, pasty, pbptyper, seqsero2, seroba, shigapass, * shigatyper, shigeifinder, sistr, ssuissero, staphtyper, stecfinder, tbprofiler * * @input record(meta, fna, r1?, r2?, se?, lr?) @@ -42,6 +42,9 @@ * @input staphtyper_repeat_order * Staphylococcus aureus repeat order file for spa typing (optional) * + * @input staphscan_db_mlst + * Custom MLST database directory for StaphSCAN surveillance (optional) + * * @output sample_outputs * Mixed per-sample records from merlindist and all activated species-specific typing * subworkflows (e.g., ectyper, sistr, kleborate). Each record carries tool-specific fields. @@ -85,6 +88,7 @@ workflow MERLIN { hicap_model_fp: Path? staphtyper_repeats: Path? staphtyper_repeat_order: Path? + staphscan_db_mlst: Path? main: // ID potential species @@ -141,7 +145,7 @@ workflow MERLIN { // Staphylococcus ch_staphylococcus = ch_merlindist.sample_outputs.filter { r -> r.staphylococcus != null } - ch_staphtyper = STAPHTYPER(ch_staphylococcus.map(forAssembly), staphtyper_repeats, staphtyper_repeat_order) + ch_staphtyper = STAPHTYPER(ch_staphylococcus.map(forAssembly), staphtyper_repeats, staphtyper_repeat_order, staphscan_db_mlst) // Streptococcus ch_streptococcus = ch_merlindist.sample_outputs.filter { r -> r.streptococcus != null } diff --git a/subworkflows/staphtyper/main.nf b/subworkflows/staphtyper/main.nf index 72177699c..3340b59e1 100644 --- a/subworkflows/staphtyper/main.nf +++ b/subworkflows/staphtyper/main.nf @@ -1,18 +1,19 @@ /** - * Determine the agr, spa and SCCmec types for _Staphylococcus aureus_ genomes. + * Determine the agr, spa, SCCmec types and perform genome-based surveillance for _Staphylococcus aureus_ genomes. * * This subworkflow performs comprehensive typing of *Staphylococcus aureus* genomes by * determining the agr locus type using [AgrVATE](https://github.com/VishnuRaghuram94/AgrVATE), - * spa repeat type using [spaTyper](https://github.com/HCGB-IGTP/spaTyper), and SCCmec element - * type using SCCmec typing. It combines results from multiple typing methods to provide - * a complete characterization of *S. aureus* strains. + * spa repeat type using [spaTyper](https://github.com/HCGB-IGTP/spaTyper), SCCmec element + * type using SCCmec typing, and genome-based surveillance using + * [StaphSCAN](https://github.com/riccabolla/StaphSCAN). It combines results from multiple + * typing and surveillance methods to provide a complete characterization of *S. aureus* strains. * * @status stable - * @keywords staphylococcus aureus, agr typing, spa typing, sccmec, strain characterization + * @keywords staphylococcus aureus, agr typing, spa typing, sccmec, surveillance, strain characterization * @tags complexity:moderate input-type:multiple output-type:multiple features:aggregation,database-dependent - * @citation agrvate, spatyper, sccmec + * @citation agrvate, sccmec, spatyper, staphscan * - * @subworkflows agrvate, spatyper, sccmec + * @subworkflows agrvate, sccmec, spatyper, staphscan * * @input record(meta, assembly) * - `meta`: Groovy Record containing sample information @@ -24,6 +25,9 @@ * @input repeat_order * Optional spa repeat order file for improved spa typing * + * @input staphscan_db_mlst + * Custom MLST database directory for StaphSCAN (optional) + * * @output sample_outputs * * @output run_outputs @@ -31,15 +35,17 @@ */ nextflow.enable.types = true -include { AGRVATE } from '../agrvate/main' -include { SPATYPER } from '../spatyper/main' -include { SCCMEC } from '../sccmec/main' +include { AGRVATE } from '../agrvate/main' +include { SPATYPER } from '../spatyper/main' +include { SCCMEC } from '../sccmec/main' +include { STAPHSCAN } from '../staphscan/main' workflow STAPHTYPER { take: assembly: Channel repeats: Path? repeat_order: Path? + staphscan_db_mlst: Path? main: // agrvate - agr locus type and agr operon variants @@ -51,8 +57,11 @@ workflow STAPHTYPER { // sccmec - SCCmec type based on targets and full cassettes ch_sccmec = SCCMEC(assembly) + // staphscan - genome-based surveillance + ch_staphscan = STAPHSCAN(assembly, staphscan_db_mlst) + emit: // Published outputs - sample_outputs = ch_agrvate.sample_outputs.mix(ch_spatyper.sample_outputs, ch_sccmec.sample_outputs) - run_outputs = ch_agrvate.run_outputs.mix(ch_spatyper.run_outputs, ch_sccmec.run_outputs) + sample_outputs = ch_agrvate.sample_outputs.mix(ch_sccmec.sample_outputs, ch_spatyper.sample_outputs, ch_staphscan.sample_outputs) + run_outputs = ch_agrvate.run_outputs.mix(ch_sccmec.run_outputs, ch_spatyper.run_outputs, ch_staphscan.run_outputs) } diff --git a/workflows/bactopia-tools/merlin/main.nf b/workflows/bactopia-tools/merlin/main.nf index 6e881c660..3caa66281 100644 --- a/workflows/bactopia-tools/merlin/main.nf +++ b/workflows/bactopia-tools/merlin/main.nf @@ -31,6 +31,9 @@ * @input spatyper_repeat_order * Path to a custom spaTyper repeat order file * + * @input staphscan_db_mlst + * Path or tarball to custom MLST database for StaphSCAN surveillance + * * @section Species-Specific Analysis * @note Tools executed depend on detected species * @publish Analysis results from all executed species-specific tools @@ -56,6 +59,7 @@ params { hicap_model_fp : Path? spatyper_repeats : Path? spatyper_repeat_order : Path? + staphscan_db_mlst : Path? } include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' @@ -77,7 +81,9 @@ workflow { params.hicap_model_fp, // staphtyper params.spatyper_repeats, - params.spatyper_repeat_order + params.spatyper_repeat_order, + // staphscan + params.staphscan_db_mlst ) publish: diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index 23eb3b288..055cf8351 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.0.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.0.0' manifest.version = "${params.bactopia_version}" // Includes @@ -54,6 +54,7 @@ includeConfig "../../../modules/ssuissero/module.config" includeConfig "../../../modules/agrvate/module.config" includeConfig "../../../modules/spatyper/module.config" includeConfig "../../../modules/sccmec/module.config" +includeConfig "../../../modules/staphscan/module.config" includeConfig "../../../modules/stecfinder/module.config" includeConfig "../../../modules/tbprofiler/profile/module.config" includeConfig "../../../modules/tbprofiler/collate/module.config" @@ -110,9 +111,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.1' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/merlin/nextflow_schema.json b/workflows/bactopia-tools/merlin/nextflow_schema.json index 16c40261d..e06262722 100644 --- a/workflows/bactopia-tools/merlin/nextflow_schema.json +++ b/workflows/bactopia-tools/merlin/nextflow_schema.json @@ -720,6 +720,27 @@ } } }, + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font" + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, "stecfinder_parameters": { "title": "STECFinder Parameters", "type": "object", @@ -1323,6 +1344,9 @@ { "$ref": "#/$defs/sccmec_parameters" }, + { + "$ref": "#/$defs/staphscan_parameters" + }, { "$ref": "#/$defs/stecfinder_parameters" }, diff --git a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap index af31f63c9..0699a75c6 100644 --- a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap @@ -386,7 +386,7 @@ ] ], - "timestamp": "2026-04-29T11:25:22.320393361", + "timestamp": "2026-05-05T13:26:46.601147931", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -394,7 +394,7 @@ }, "Merlin (--full_merlin) - portiera|compressed_fasta_and_fastq": { "content": [ - 48, + 50, [ "SRR2838702", "SRR2838702/tools", @@ -679,6 +679,17 @@ "SRR2838702/tools/ssuissero/logs/nf.command.sh", "SRR2838702/tools/ssuissero/logs/nf.command.trace", "SRR2838702/tools/ssuissero/logs/versions.yml", + "SRR2838702/tools/staphscan", + "SRR2838702/tools/staphscan/SRR2838702.tsv", + "SRR2838702/tools/staphscan/logs", + "SRR2838702/tools/staphscan/logs/nf.command.begin", + "SRR2838702/tools/staphscan/logs/nf.command.err", + "SRR2838702/tools/staphscan/logs/nf.command.log", + "SRR2838702/tools/staphscan/logs/nf.command.out", + "SRR2838702/tools/staphscan/logs/nf.command.run", + "SRR2838702/tools/staphscan/logs/nf.command.sh", + "SRR2838702/tools/staphscan/logs/nf.command.trace", + "SRR2838702/tools/staphscan/logs/versions.yml", "SRR2838702/tools/stecfinder", "SRR2838702/tools/stecfinder/SRR2838702.tsv", "SRR2838702/tools/stecfinder/logs", @@ -909,6 +920,15 @@ "bactopia-runs/merlin/merged-results/logs/ssuissero-concat/nf.command.sh", "bactopia-runs/merlin/merged-results/logs/ssuissero-concat/nf.command.trace", "bactopia-runs/merlin/merged-results/logs/ssuissero-concat/versions.yml", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.begin", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.err", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.log", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.out", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.run", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.sh", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/nf.command.trace", + "bactopia-runs/merlin/merged-results/logs/staphscan-concat/versions.yml", "bactopia-runs/merlin/merged-results/logs/stecfinder-concat", "bactopia-runs/merlin/merged-results/logs/stecfinder-concat/nf.command.begin", "bactopia-runs/merlin/merged-results/logs/stecfinder-concat/nf.command.err", @@ -939,6 +959,7 @@ "bactopia-runs/merlin/merged-results/sistr.tsv", "bactopia-runs/merlin/merged-results/spatyper.tsv", "bactopia-runs/merlin/merged-results/ssuissero.tsv", + "bactopia-runs/merlin/merged-results/staphscan.tsv", "bactopia-runs/merlin/merged-results/stecfinder.tsv", "bactopia-runs/merlin/merged-results/tbprofiler.csv", "bactopia-runs/merlin/merged-results/tbprofiler.variants.csv", @@ -952,7 +973,7 @@ ] ], - "timestamp": "2026-04-29T11:27:06.08576866", + "timestamp": "2026-05-05T13:27:58.035964435", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphtyper/main.nf b/workflows/bactopia-tools/staphtyper/main.nf index 94617e419..677913b49 100644 --- a/workflows/bactopia-tools/staphtyper/main.nf +++ b/workflows/bactopia-tools/staphtyper/main.nf @@ -7,11 +7,12 @@ * 1. [AgrVATE](https://github.com/VishnuRaghuram94/AgrVATE) - agr locus type and operon variants * 2. [spaTyper](https://github.com/HCGB-IGTP/spaTyper) - spa type * 3. [sccmec](https://github.com/rpetit3/sccmec) - SCCmec type + * 4. [StaphSCAN](https://github.com/riccabolla/StaphSCAN) - genome-based surveillance * * @status stable - * @keywords staphylococcus aureus, agr, spa, sccmec, typing, bactopia-tool + * @keywords staphylococcus aureus, agr, spa, sccmec, surveillance, typing, bactopia-tool * @tags complexity:moderate input-type:parameter output-type:multiple features:bactopia-tool,typing,workflow - * @citation agrvate, spatyper, sccmec + * @citation agrvate, sccmec, spatyper, staphscan * * @subworkflows utils_bactopia-tools, staphtyper * @@ -24,6 +25,9 @@ * @input spatyper_repeat_order * Path to a custom spaTyper repeat order file * + * @input staphscan_db_mlst + * Path or tarball to custom MLST database for StaphSCAN + * * @section Comprehensive Typing * @note Results from all included typing tools * @publish staphtyper.tsv Merged summary containing agr, spa, and SCCmec typing results @@ -43,6 +47,7 @@ params { // Tool-specific parameters spatyper_repeats : Path? spatyper_repeat_order : Path? + staphscan_db_mlst : Path? } include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' @@ -55,7 +60,8 @@ workflow { ch_staphtyper = STAPHTYPER( ch_bactopiatool.assembly, params.spatyper_repeats, - params.spatyper_repeat_order + params.spatyper_repeat_order, + params.staphscan_db_mlst ) publish: diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 38449328b..7d4c3008f 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.0.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.0.0' manifest.version = "${params.bactopia_version}" // Includes @@ -32,6 +32,7 @@ includeConfig "../../../modules/csvtk/concat/module.config" includeConfig "../../../modules/agrvate/module.config" includeConfig "../../../modules/spatyper/module.config" includeConfig "../../../modules/sccmec/module.config" +includeConfig "../../../modules/staphscan/module.config" // Set output directory outputDir = params.outdir @@ -85,9 +86,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.1' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/staphtyper/nextflow_schema.json b/workflows/bactopia-tools/staphtyper/nextflow_schema.json index 2fefd780f..ea891890d 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow_schema.json +++ b/workflows/bactopia-tools/staphtyper/nextflow_schema.json @@ -133,6 +133,27 @@ } } }, + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font" + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, "optional_parameters": { "title": "Optional Parameters", "type": "object", @@ -494,6 +515,9 @@ { "$ref": "#/$defs/sccmec_parameters" }, + { + "$ref": "#/$defs/staphscan_parameters" + }, { "$ref": "#/$defs/optional_parameters" }, diff --git a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap index f92fb0f65..3c29ccbe1 100644 --- a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap @@ -1,7 +1,7 @@ { "staphtyper - GCF_000017085|staphylococcus_aureus|compressed_fasta": { "content": [ - 6, + 8, [ "GCF_000017085", "GCF_000017085/tools", @@ -46,6 +46,17 @@ "GCF_000017085/tools/spatyper/logs/nf.command.sh", "GCF_000017085/tools/spatyper/logs/nf.command.trace", "GCF_000017085/tools/spatyper/logs/versions.yml", + "GCF_000017085/tools/staphscan", + "GCF_000017085/tools/staphscan/GCF_000017085.tsv", + "GCF_000017085/tools/staphscan/logs", + "GCF_000017085/tools/staphscan/logs/nf.command.begin", + "GCF_000017085/tools/staphscan/logs/nf.command.err", + "GCF_000017085/tools/staphscan/logs/nf.command.log", + "GCF_000017085/tools/staphscan/logs/nf.command.out", + "GCF_000017085/tools/staphscan/logs/nf.command.run", + "GCF_000017085/tools/staphscan/logs/nf.command.sh", + "GCF_000017085/tools/staphscan/logs/nf.command.trace", + "GCF_000017085/tools/staphscan/logs/versions.yml", "bactopia-runs", "bactopia-runs/staphtyper", "bactopia-runs/staphtyper/merged-results", @@ -78,8 +89,18 @@ "bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf.command.sh", "bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/nf.command.trace", "bactopia-runs/staphtyper/merged-results/logs/spatyper-concat/versions.yml", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.begin", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.err", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.log", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.out", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.run", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.sh", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/nf.command.trace", + "bactopia-runs/staphtyper/merged-results/logs/staphscan-concat/versions.yml", "bactopia-runs/staphtyper/merged-results/sccmec.tsv", "bactopia-runs/staphtyper/merged-results/spatyper.tsv", + "bactopia-runs/staphtyper/merged-results/staphscan.tsv", "bactopia-runs/staphtyper/nf-reports", "bactopia-runs/staphtyper/nf-reports/staphtyper-dag.dot", "bactopia-runs/staphtyper/nf-reports/staphtyper-report.html", @@ -99,15 +120,19 @@ "versions.yml:md5,4d90b86147c4eb115fc93edc4fa484b8", "GCF_000017085.tsv:md5,6afe7a90c591e32107d86c0e81029f54", "versions.yml:md5,32d57feabda90e9fe6e0aeb96e5d2352", + "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + "versions.yml:md5,9048a4caf373fcb35bb1f990c90ddcf0", "agrvate.tsv:md5,6acd3d01fc9d867f32435265331ff7b2", "versions.yml:md5,d203f21af354f31f3d144e58af47cff3", "versions.yml:md5,35f4a9f839e9fd13b2afb63fecea88b4", "versions.yml:md5,db2a4ba0c195fd025b9a8068ad991793", + "versions.yml:md5,c707d4291d068c2b150937480568d0b0", "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975", - "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" + "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54", + "staphscan.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb" ] ], - "timestamp": "2026-04-29T11:24:45.385204274", + "timestamp": "2026-05-05T13:24:58.587861386", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/staphopia/main.nf b/workflows/staphopia/main.nf index b5052aaaf..d7930777c 100644 --- a/workflows/staphopia/main.nf +++ b/workflows/staphopia/main.nf @@ -5,7 +5,8 @@ * This workflow performs complete bacterial analysis including quality control, * assembly, annotation, antimicrobial resistance detection, MLST typing, * and Staphylococcus-specific analysis using [Spatyper](https://github.com/HCGB-IGTP/spaTyper), - * [AgrVATE](https://github.com/VishnuRaghuram94/AgrVATE), and [SCCmecFinder](https://github.com/rpetit3/sccmec). + * [AgrVATE](https://github.com/VishnuRaghuram94/AgrVATE), [SCCmecFinder](https://github.com/rpetit3/sccmec), + * and [StaphSCAN](https://github.com/riccabolla/StaphSCAN). * It processes raw sequencing reads and produces a comprehensive genomic characterization for S. aureus isolates. * * @status stable @@ -58,6 +59,9 @@ * @input spatyper_repeat_order * Path to repeat order file for Spatyper * + * @input staphscan_db_mlst + * Path or tarball to custom MLST database for StaphSCAN + * * @section Quality Control * @publish supplemental/*_fastqc.* FastQC quality control reports for raw and cleaned reads * @publish supplemental/*-NanoPlot.* NanoPlot reports for Nanopore reads @@ -124,6 +128,7 @@ params { prokka_prodigal_tf : Path? spatyper_repeats : Path? spatyper_repeat_order : Path? + staphscan_db_mlst : Path? } // Core @@ -198,7 +203,8 @@ workflow { ch_staphtyper = STAPHTYPER( ch_assembler.assembly, params.spatyper_repeats, - params.spatyper_repeat_order + params.spatyper_repeat_order, + params.staphscan_db_mlst ) // Collect all outputs diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 0a7eb6a99..78df6242b 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.0.0' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.0.0' manifest.version = "${params.bactopia_version}" // Includes @@ -41,6 +41,7 @@ includeConfig "../../modules/prokka/module.config" includeConfig "../../modules/agrvate/module.config" includeConfig "../../modules/spatyper/module.config" includeConfig "../../modules/sccmec/module.config" +includeConfig "../../modules/staphscan/module.config" // Workflow specific params.config includeConfig "../../conf/params/staphopia.config" @@ -97,9 +98,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.1' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index f4c58f782..b84fdebfe 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -1003,6 +1003,7 @@ "properties": { "prokka_proteins": { "type": "string", + "default": "${projectDir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font", "hidden": true @@ -1138,6 +1139,28 @@ } } }, + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font", + "hidden": true + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, "optional_parameters": { "title": "Optional Parameters", "type": "object", @@ -1526,6 +1549,9 @@ { "$ref": "#/$defs/sccmec_parameters" }, + { + "$ref": "#/$defs/staphscan_parameters" + }, { "$ref": "#/$defs/optional_parameters" }, diff --git a/workflows/staphopia/tests/main.nf.test.snap b/workflows/staphopia/tests/main.nf.test.snap index 077ef9762..346c80ece 100644 --- a/workflows/staphopia/tests/main.nf.test.snap +++ b/workflows/staphopia/tests/main.nf.test.snap @@ -1,7 +1,7 @@ { "Staphopia (pe) - SRR2838702|portiera|illumina": { "content": [ - 17, + 19, [ "SRR2838702", "SRR2838702/main", @@ -167,6 +167,17 @@ "SRR2838702/tools/spatyper/logs/nf.command.sh", "SRR2838702/tools/spatyper/logs/nf.command.trace", "SRR2838702/tools/spatyper/logs/versions.yml", + "SRR2838702/tools/staphscan", + "SRR2838702/tools/staphscan/SRR2838702.tsv", + "SRR2838702/tools/staphscan/logs", + "SRR2838702/tools/staphscan/logs/nf.command.begin", + "SRR2838702/tools/staphscan/logs/nf.command.err", + "SRR2838702/tools/staphscan/logs/nf.command.log", + "SRR2838702/tools/staphscan/logs/nf.command.out", + "SRR2838702/tools/staphscan/logs/nf.command.run", + "SRR2838702/tools/staphscan/logs/nf.command.sh", + "SRR2838702/tools/staphscan/logs/nf.command.trace", + "SRR2838702/tools/staphscan/logs/versions.yml", "bactopia-runs", "bactopia-runs/staphopia", "bactopia-runs/staphopia/merged-results", @@ -237,10 +248,20 @@ "bactopia-runs/staphopia/merged-results/logs/spatyper-concat/nf.command.sh", "bactopia-runs/staphopia/merged-results/logs/spatyper-concat/nf.command.trace", "bactopia-runs/staphopia/merged-results/logs/spatyper-concat/versions.yml", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.begin", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.err", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.log", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.out", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.run", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.sh", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/nf.command.trace", + "bactopia-runs/staphopia/merged-results/logs/staphscan-concat/versions.yml", "bactopia-runs/staphopia/merged-results/meta.tsv", "bactopia-runs/staphopia/merged-results/mlst.tsv", "bactopia-runs/staphopia/merged-results/sccmec.tsv", "bactopia-runs/staphopia/merged-results/spatyper.tsv", + "bactopia-runs/staphopia/merged-results/staphscan.tsv", "bactopia-runs/staphopia/nf-reports", "bactopia-runs/staphopia/nf-reports/staphopia-dag.dot", "bactopia-runs/staphopia/nf-reports/staphopia-report.html", @@ -257,16 +278,18 @@ "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee", "versions.yml:md5,4d90b86147c4eb115fc93edc4fa484b8", "versions.yml:md5,32d57feabda90e9fe6e0aeb96e5d2352", + "versions.yml:md5,9048a4caf373fcb35bb1f990c90ddcf0", "versions.yml:md5,d203f21af354f31f3d144e58af47cff3", "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6", "versions.yml:md5,1913efda4329af168df4ab88555dbeb4", "versions.yml:md5,61924107a406c136f55c445d470721f7", "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc", "versions.yml:md5,35f4a9f839e9fd13b2afb63fecea88b4", - "versions.yml:md5,db2a4ba0c195fd025b9a8068ad991793" + "versions.yml:md5,db2a4ba0c195fd025b9a8068ad991793", + "versions.yml:md5,c707d4291d068c2b150937480568d0b0" ] ], - "timestamp": "2026-04-29T11:29:39.249406285", + "timestamp": "2026-05-05T13:34:09.075806826", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 06d0af1678b4cb0424e9173c48da48c441bb3b17 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 5 May 2026 13:42:27 -0600 Subject: [PATCH 05/43] fix version numbers --- workflows/bactopia-tools/merlin/nextflow.config | 8 ++++---- workflows/bactopia-tools/staphscan/nextflow.config | 2 +- workflows/bactopia-tools/staphtyper/nextflow.config | 8 ++++---- workflows/staphopia/nextflow.config | 8 ++++---- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index 055cf8351..d76a05693 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -111,9 +111,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.3' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index 1b2b14e18..945068486 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 7d4c3008f..fe9665dbd 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -86,9 +86,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.3' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 78df6242b..bf6161722 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.0' + version = '4.0.1' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.0' +params.bactopia_version = '4.0.1' manifest.version = "${params.bactopia_version}" // Includes @@ -98,9 +98,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.1' + id 'nf-bactopia@2.1.3' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} From 68e9efd26696032650c1c31c61221b37d804b601 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 09:06:20 -0600 Subject: [PATCH 06/43] add bactopia tool for traitar --- catalog.json | 101 +++- conf/test.config | 1 + data/citations.yml | 7 + llms.txt | 4 +- modules/traitar/download/main.nf | 58 +++ modules/traitar/download/module.config | 29 ++ modules/traitar/download/schema.json | 35 ++ modules/traitar/run/main.nf | 118 +++++ modules/traitar/run/module.config | 22 + modules/traitar/run/schema.json | 22 + modules/traitar/run/tests/main.nf.test | 74 +++ modules/traitar/run/tests/main.nf.test.snap | 42 ++ modules/traitar/run/tests/nextflow.config | 36 ++ modules/traitar/run/tests/nf-test.config | 11 + subworkflows/traitar/main.nf | 62 +++ subworkflows/traitar/tests/.nftignore | 2 + subworkflows/traitar/tests/main.nf.test | 48 ++ subworkflows/traitar/tests/main.nf.test.snap | 33 ++ subworkflows/traitar/tests/nextflow.config | 41 ++ subworkflows/traitar/tests/nf-test.config | 11 + workflows/bactopia-tools/traitar/main.nf | 91 ++++ .../bactopia-tools/traitar/nextflow.config | 92 ++++ .../traitar/nextflow_schema.json | 453 ++++++++++++++++++ .../bactopia-tools/traitar/tests/.nftignore | 5 + .../bactopia-tools/traitar/tests/main.nf.test | 43 ++ .../traitar/tests/main.nf.test.snap | 77 +++ .../traitar/tests/nf-test.config | 11 + 27 files changed, 1526 insertions(+), 3 deletions(-) create mode 100644 modules/traitar/download/main.nf create mode 100644 modules/traitar/download/module.config create mode 100644 modules/traitar/download/schema.json create mode 100644 modules/traitar/run/main.nf create mode 100644 modules/traitar/run/module.config create mode 100644 modules/traitar/run/schema.json create mode 100644 modules/traitar/run/tests/main.nf.test create mode 100644 modules/traitar/run/tests/main.nf.test.snap create mode 100644 modules/traitar/run/tests/nextflow.config create mode 100644 modules/traitar/run/tests/nf-test.config create mode 100644 subworkflows/traitar/main.nf create mode 100644 subworkflows/traitar/tests/.nftignore create mode 100644 subworkflows/traitar/tests/main.nf.test create mode 100644 subworkflows/traitar/tests/main.nf.test.snap create mode 100644 subworkflows/traitar/tests/nextflow.config create mode 100644 subworkflows/traitar/tests/nf-test.config create mode 100644 workflows/bactopia-tools/traitar/main.nf create mode 100644 workflows/bactopia-tools/traitar/nextflow.config create mode 100644 workflows/bactopia-tools/traitar/nextflow_schema.json create mode 100644 workflows/bactopia-tools/traitar/tests/.nftignore create mode 100644 workflows/bactopia-tools/traitar/tests/main.nf.test create mode 100644 workflows/bactopia-tools/traitar/tests/main.nf.test.snap create mode 100644 workflows/bactopia-tools/traitar/tests/nf-test.config diff --git a/catalog.json b/catalog.json index baaebeade..b5b0f831d 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-05-05T19:22:52Z", + "generated": "2026-05-06T14:51:44Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.1.6", "nf_bactopia_version": "2.1.3", @@ -2931,6 +2931,55 @@ "conditional-logic" ] } + }, + "traitar_download": { + "description": "Download the Pfam database required by Traitar.", + "path": "modules/traitar/download/", + "scope": "run", + "process_name": "traitar_download", + "tool": { + "name": "traitar", + "version": "3.0.1" + }, + "emits": [ + "db" + ], + "tags": { + "complexity": "simple", + "input_type": "none", + "output_type": "single", + "features": [ + "internet-access", + "resource-download", + "no-test" + ] + } + }, + "traitar_run": { + "description": "Predict phenotypic traits from microbial genomes.", + "path": "modules/traitar/run/", + "scope": "sample", + "process_name": "traitar", + "tool": { + "name": "traitar", + "version": "3.0.1" + }, + "takes": [ + "fna" + ], + "emits": [ + "majority_tsv", + "single_tsv" + ], + "tags": { + "complexity": "simple", + "input_type": "single", + "output_type": "single", + "features": [ + "database-dependent", + "conditional-logic" + ] + } } }, "subworkflows": { @@ -6220,6 +6269,45 @@ "conditional-logic" ] } + }, + "traitar": { + "description": "Predict phenotypic traits from microbial genomes", + "path": "subworkflows/traitar/", + "takes": [ + "fna" + ], + "takes_params": [ + "database", + "download_traitar" + ], + "emits": { + "sample_outputs": [ + "majority_tsv", + "single_tsv" + ], + "run_outputs": [ + "csv" + ] + }, + "scope": "sample", + "calls": { + "modules": [ + "traitar_download", + "traitar_run", + "csvtk_concat" + ] + }, + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "aggregation", + "database-dependent", + "conditional-logic", + "resource-download" + ] + } } }, "workflows": { @@ -6993,6 +7081,17 @@ "tbprofiler" ] }, + "traitar": { + "description": "Predict phenotypic traits from microbial genomes", + "type": "tool", + "path": "workflows/bactopia-tools/traitar/", + "ext": [ + "fna" + ], + "subworkflows": [ + "traitar" + ] + }, "cleanyerreads": { "description": "Quality control and optional host read removal from raw sequencing reads.", "type": "named", diff --git a/conf/test.config b/conf/test.config index 424b64a7d..b3aab0cec 100644 --- a/conf/test.config +++ b/conf/test.config @@ -53,6 +53,7 @@ params { sylph_db = "${params.test_data_dir}/${params.test_dataset}" tblastn_query = "${params.test_data_dir}/${params.test_dataset}" tblastx_query = "${params.test_data_dir}/${params.test_dataset}" + traitar_db = "${params.test_data_dir}/${params.test_dataset}" // Static data inputs prokka_proteins = "${params.test_data_dir}/datasets/generic/proteins.faa" diff --git a/data/citations.yml b/data/citations.yml index 9ec1d3727..c56927566 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -1073,6 +1073,13 @@ tools: cite: | Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG [Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs.](https://doi.org/10.1186/s13073-019-0650-x) _Genome Med_ 11, 41 (2019) + traitar: + name: Traitar + link: https://github.com/nick-youngblut/traitar3/ + description: Predict phenotypic traits from microbial genomes + cite: | + Weimann A, Mooren K, Frank J, Pope PB, Gronow S, So AP [From genomes to phenotypes: Traitar, the microbial trait analyzer.](https://doi.org/10.1128/mSystems.00101-16) _mSystems_ 1(6), e00101-16 (2016) + unicycler: name: Unicycler link: https://github.com/rrwick/Unicycler diff --git a/llms.txt b/llms.txt index 69277502e..b7df9cbf5 100644 --- a/llms.txt +++ b/llms.txt @@ -23,7 +23,7 @@ All components use standardized GroovyDoc documentation and static typing. - [workflows/cleanyerreads/](workflows/cleanyerreads/): Quality control and optional host read removal from raw sequencing reads. - [workflows/staphopia/](workflows/staphopia/): Comprehensive analysis pipeline for Staphylococcus aureus isolates. - [workflows/teton/](workflows/teton/): Taxonomic classification and abundance profiling of metagenomic reads. -- [workflows/bactopia-tools/](workflows/bactopia-tools/): 68 comparative analysis workflows (pan-genome, phylogenetics, typing) +- [workflows/bactopia-tools/](workflows/bactopia-tools/): 69 comparative analysis workflows (pan-genome, phylogenetics, typing) ## Subworkflows (Tier 2) @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -99 tool-specific modules live under `modules/`. Each module directory contains: +101 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/traitar/download/main.nf b/modules/traitar/download/main.nf new file mode 100644 index 000000000..304fd94eb --- /dev/null +++ b/modules/traitar/download/main.nf @@ -0,0 +1,58 @@ +/** + * Download the Pfam database required by Traitar. + * + * Fetches the pre-compiled Pfam database required by [Traitar](https://github.com/nick-youngblut/traitar3/) + * for microbial phenotype prediction. The database contains Pfam HMM models used for + * protein family annotation during trait prediction. + * + * @status stable + * @keywords phenotype, traits, pfam, database, download + * @tags complexity:simple input-type:none output-type:single features:internet-access,resource-download,no-test + * @citation traitar + * + * @note Internet & Storage Required + * This process requires an active internet connection and significant disk space + * to store the Pfam database files (~1.2GB). + * + * @output record(db, logs) + * - `db`: The Pfam-A HMM file for Traitar + */ +nextflow.enable.types = true + +// bactopia-lint: ignore M012,M017,M018,M023,M024,M025,M026,M028,M033 +process TRAITAR_DOWNLOAD { + label 'process_low' + label 'process_long' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + output: + record( + db: file("Pfam-A.hmm"), + logs: files("logs/*", optional: true) + ) + + script: + """ + traitar pfam pfam_data + mv pfam_data/Pfam-A.hmm Pfam-A.hmm + + # Move outputs to tool specific folder + mkdir -p logs + cp .command.begin logs/nf.command.begin + cp .command.err logs/nf.command.err + cp .command.log logs/nf.command.log + cp .command.out logs/nf.command.out + cp .command.run logs/nf.command.run + cp .command.sh logs/nf.command.sh + cp .command.trace logs/nf.command.trace + + # Cleanup + + cat <<-END_VERSIONS > logs/versions.yml + "${task.process}": + traitar: \$( traitar --version 2>&1 | tail -1 ) + END_VERSIONS + """ +} diff --git a/modules/traitar/download/module.config b/modules/traitar/download/module.config new file mode 100644 index 000000000..3ea704c9c --- /dev/null +++ b/modules/traitar/download/module.config @@ -0,0 +1,29 @@ +params { + // traitar_download + download_traitar = false + traitar_db = "" +} + +process { + withName: 'TRAITAR_DOWNLOAD' { + ext.wf = params.wf + ext.scope = "run" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "traitar_download" + publishDir = [[ + path: params.traitar_db, + mode: params.publish_dir_mode, + overwrite: true + ]] + + // Tool arguments + ext.args = "" + + // Environment information + ext.toolName = "bioconda::traitar=3.0.1".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/traitar:3.0.1--pyhdfd78af_1" + ext.image = "https://depot.galaxyproject.org/singularity/traitar:3.0.1--pyhdfd78af_1" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/traitar/download/schema.json b/modules/traitar/download/schema.json new file mode 100644 index 000000000..72d94b49b --- /dev/null +++ b/modules/traitar/download/schema.json @@ -0,0 +1,35 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/traitar/download/schema.json", + "title": "Traitar Download Module", + "description": "A module for downloading the Pfam database required by Traitar", + "type": "object", + "$defs": { + "traitar_download_parameters": { + "title": "Traitar Download Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "traitar_db": { + "type": "string", + "description": "Path to the Pfam-A HMM file for Traitar", + "fa_icon": "fas fa-font", + "is_required": true + }, + "download_traitar": { + "type": "boolean", + "description": "Download the Pfam database to the path given by --traitar_db", + "default": false, + "fa_icon": "fas fa-toggle-on" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/traitar_download_parameters" + } + ] +} diff --git a/modules/traitar/run/main.nf b/modules/traitar/run/main.nf new file mode 100644 index 000000000..33907d103 --- /dev/null +++ b/modules/traitar/run/main.nf @@ -0,0 +1,118 @@ +/** + * Predict phenotypic traits from microbial genomes. + * + * Uses [Traitar](https://github.com/nick-youngblut/traitar3/) to predict phenotypic + * traits from nucleotide sequences. Traitar annotates protein families using Pfam and + * applies machine learning models to predict 67 diverse microbial traits. + * + * @status stable + * @keywords phenotype, traits, pfam + * @tags complexity:simple input-type:single output-type:single features:database-dependent,conditional-logic + * @citation traitar + * + * @note Database Required + * Requires a Pfam database directory (downloaded via `traitar pfam` or the download module). + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @input db + * Pfam-A HMM file for Traitar + * + * @output record(meta, majority_tsv, single_tsv, results, logs, nf_logs, versions) + * - `majority_tsv`: Majority-vote combined phenotype trait predictions + * - `single_tsv`: Single-votes combined phenotype trait predictions + */ +nextflow.enable.types = true + +process TRAITAR_RUN { + tag "${prefix}" + label 'process_low' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + record ( + meta: Record, + fna: Path + ) + db: Path + + output: + record( + // Named fields (used downstream) + meta: meta, + majority_tsv: file("${prefix}.majority.tsv"), + single_tsv: file("${prefix}.single_votes.tsv"), + // Generic fields (used for publishing) + results: [ + files("${prefix}.majority.tsv"), + files("${prefix}.single_votes.tsv"), + files("supplemental/*") + ], + logs: files("*.{log,err}", optional: true), + nf_logs: files(".command.*"), + versions: files("versions.yml") + ) + + script: + def _meta = meta + prefix = task.ext.prefix ?: "${_meta.name}" + + // Create a new meta record + meta = record( + id: "${prefix}-${task.process}", + name: prefix, + scope: task.ext.scope, + output_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}", + logs_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}/logs/${task.ext.logs_subdir}", + process_name: task.ext.process_name + ) + + def is_compressed = fna.getName().endsWith(".gz") ? true : false + def fna_name = fna.getName().replace(".gz", "") + """ + # Decompress input if needed + if [ "${is_compressed}" == "true" ]; then + gzip -c -d ${fna} > ${fna_name} + else + cp -L ${fna} ${fna_name} + fi + + # Create input directory and sample file for traitar + mkdir -p input_dir + mv ${fna_name} input_dir/ + + cat > samples.tsv <<-SAMPLE_EOF + sample_file_name\tsample_name + ${fna_name}\t${prefix} + SAMPLE_EOF + + # Run traitar phenotype prediction + traitar phenotype \\ + ${db} \\ + input_dir \\ + samples.tsv \\ + from_nucleotides \\ + ${prefix} \\ + -c ${task.cpus} \\ + --overwrite \\ + ${task.ext.args} + + # Rename primary output for consistency + mkdir supplemental + mv ${prefix}/* supplemental/ + mv supplemental/phenotype_prediction/predictions_majority-vote_combined.txt ${prefix}.majority.tsv + mv supplemental/phenotype_prediction/predictions_single-votes_combined.txt ${prefix}.single_votes.tsv + + # Cleanup + rm -rf input_dir/ samples.tsv ${prefix}/ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + traitar: \$( traitar --version 2>&1 | tail -1 ) + END_VERSIONS + """ +} diff --git a/modules/traitar/run/module.config b/modules/traitar/run/module.config new file mode 100644 index 000000000..ffdf6e8b2 --- /dev/null +++ b/modules/traitar/run/module.config @@ -0,0 +1,22 @@ +params { + // traitar_run +} + +process { + withName: 'TRAITAR_RUN' { + ext.wf = params.wf + ext.scope = "sample" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "traitar" + + // Tool arguments + ext.args = "" + + // Environment information + ext.toolName = "bioconda::traitar=3.0.1".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/traitar:3.0.1--pyhdfd78af_1" + ext.image = "https://depot.galaxyproject.org/singularity/traitar:3.0.1--pyhdfd78af_1" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/traitar/run/schema.json b/modules/traitar/run/schema.json new file mode 100644 index 000000000..c059cfb6d --- /dev/null +++ b/modules/traitar/run/schema.json @@ -0,0 +1,22 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/traitar/run/schema.json", + "title": "Traitar Module", + "description": "A module for predicting phenotypic traits from microbial genomes", + "type": "object", + "$defs": { + "traitar_parameters": { + "title": "Traitar Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": {} + } + }, + "allOf": [ + { + "$ref": "#/$defs/traitar_parameters" + } + ] +} diff --git a/modules/traitar/run/tests/main.nf.test b/modules/traitar/run/tests/main.nf.test new file mode 100644 index 000000000..21172d8eb --- /dev/null +++ b/modules/traitar/run/tests/main.nf.test @@ -0,0 +1,74 @@ +nextflow_process { + name "Test TRAITAR_RUN" + script "../main.nf" + process "TRAITAR_RUN" + tag "modules" + tag "traitar" + tag "traitar_run" + + test("traitar - module - GCF_000017085") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_000017085"], + fna: file("${params.test_data_dir}/species/staphylococcus_aureus/uncompressed/GCF_000017085/main/assembler/GCF_000017085.fna") + ) + ) + input[1] = file("${params.test_data_dir}/datasets/traitar") + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.versions + ).match() }, + { assert record.majority_tsv != null }, + { assert record.single_tsv != null }, + { assert record.results != null } + ) + } + } + + test("traitar - module - GCF_000017085 - gz") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_000017085"], + fna: file("${params.test_data_dir}/species/staphylococcus_aureus/compressed/GCF_000017085/main/assembler/GCF_000017085.fna.gz") + ) + ) + input[1] = file("${params.test_data_dir}/datasets/traitar") + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.versions + ).match() }, + { assert record.majority_tsv != null }, + { assert record.single_tsv != null }, + { assert record.results != null } + ) + } + } +} diff --git a/modules/traitar/run/tests/main.nf.test.snap b/modules/traitar/run/tests/main.nf.test.snap new file mode 100644 index 000000000..dba1061f2 --- /dev/null +++ b/modules/traitar/run/tests/main.nf.test.snap @@ -0,0 +1,42 @@ +{ + "traitar - module - GCF_000017085": { + "content": [ + { + "id": "GCF_000017085-TRAITAR_RUN", + "logs_dir": "GCF_000017085/tools/traitar//logs/", + "name": "GCF_000017085", + "output_dir": "GCF_000017085/tools/traitar/", + "process_name": "traitar", + "scope": "sample" + }, + [ + "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" + ] + ], + "timestamp": "2026-05-06T08:19:10.186774203", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "traitar - module - GCF_000017085 - gz": { + "content": [ + { + "id": "GCF_000017085-TRAITAR_RUN", + "logs_dir": "GCF_000017085/tools/traitar//logs/", + "name": "GCF_000017085", + "output_dir": "GCF_000017085/tools/traitar/", + "process_name": "traitar", + "scope": "sample" + }, + [ + "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" + ] + ], + "timestamp": "2026-05-06T08:22:03.435009482", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/traitar/run/tests/nextflow.config b/modules/traitar/run/tests/nextflow.config new file mode 100644 index 000000000..35a2ab164 --- /dev/null +++ b/modules/traitar/run/tests/nextflow.config @@ -0,0 +1,36 @@ +// Minimal config for module-level testing of TRAITAR_RUN +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "traitar" + logo_name = "bactopia-tools" + description = "Predict phenotypic traits from microbial genomes" + ext = "fna" + } + + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +includeConfig "../module.config" +includeConfig "../../../../conf/base.config" +includeConfig "../../../../conf/profiles.config" diff --git a/modules/traitar/run/tests/nf-test.config b/modules/traitar/run/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/modules/traitar/run/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/subworkflows/traitar/main.nf b/subworkflows/traitar/main.nf new file mode 100644 index 000000000..8111886db --- /dev/null +++ b/subworkflows/traitar/main.nf @@ -0,0 +1,62 @@ +/** + * Predict phenotypic traits from microbial genomes + * + * This subworkflow uses [Traitar](https://github.com/nick-youngblut/traitar3/) to predict phenotypic traits from microbial genomes. + * It can download and prepare the Pfam database on-demand or use a pre-existing database. + * It processes each sample individually and aggregates the results into + * a single consolidated report. + * + * @status stable + * @keywords phenotype, traits, pfam + * @tags complexity:moderate input-type:single output-type:multiple features:aggregation,database-dependent,conditional-logic,resource-download + * @citation traitar + * + * @modules csvtk_concat, traitar_download, traitar_run + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @input database + * Optional pre-existing Pfam-A HMM file + * + * @input download_traitar + * Boolean flag to trigger automatic database download + * + * @output sample_outputs + * - `majority_tsv`: Majority-vote combined phenotype trait predictions + * - `single_tsv`: Single-votes combined phenotype trait predictions + * + * @output run_outputs + * - `csv`: Merged TSV files with traitar majority-vote and single-vote results from all samples + */ +nextflow.enable.types = true + +include { TRAITAR_DOWNLOAD } from '../../modules/traitar/download/main' +include { TRAITAR_RUN } from '../../modules/traitar/run/main' +include { CSVTK_CONCAT as CSVTK_CONCAT_MAJORITY } from '../../modules/csvtk/concat/main' +include { CSVTK_CONCAT as CSVTK_CONCAT_SINGLE } from '../../modules/csvtk/concat/main' +include { gatherCsvtk } from 'plugin/nf-bactopia' + +workflow TRAITAR { + take: + fna: Channel + database: Path? + download_traitar: Boolean + + main: + ch_traitar_run = channel.empty() + if (download_traitar) { + ch_traitar_download = TRAITAR_DOWNLOAD() + ch_traitar_run = TRAITAR_RUN(fna, ch_traitar_download.map { r -> r.db }) + } else { + ch_traitar_run = TRAITAR_RUN(fna, database) + } + ch_majority_concat = CSVTK_CONCAT_MAJORITY(gatherCsvtk(ch_traitar_run, 'majority_tsv', [name: 'traitar-majority']), 'tsv', 'tsv') + ch_single_concat = CSVTK_CONCAT_SINGLE(gatherCsvtk(ch_traitar_run, 'single_tsv', [name: 'traitar-single']), 'tsv', 'tsv') + + emit: + // Published outputs + sample_outputs = ch_traitar_run + run_outputs = ch_majority_concat.mix(ch_single_concat) +} diff --git a/subworkflows/traitar/tests/.nftignore b/subworkflows/traitar/tests/.nftignore new file mode 100644 index 000000000..7b276dee3 --- /dev/null +++ b/subworkflows/traitar/tests/.nftignore @@ -0,0 +1,2 @@ +**/*.{err,log,stderr,stdout} +**/*.command.* diff --git a/subworkflows/traitar/tests/main.nf.test b/subworkflows/traitar/tests/main.nf.test new file mode 100644 index 000000000..69cc39f30 --- /dev/null +++ b/subworkflows/traitar/tests/main.nf.test @@ -0,0 +1,48 @@ +nextflow_workflow { + name "Test TRAITAR Subworkflow" + script "../main.nf" + workflow "TRAITAR" + tag "subworkflows" + tag "traitar" + + test("traitar - subworkflow - GCF_000017085") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_000017085"], + fna: file("${params.test_data_dir}/species/staphylococcus_aureus/compressed/GCF_000017085/main/assembler/GCF_000017085.fna.gz") + ) + ) + input[1] = file("${params.test_data_dir}/datasets/traitar") + input[2] = false + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def run = workflow.out.run_outputs[0] + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs != null }, + { assert workflow.out.run_outputs != null }, + { assert snapshot( + sample.meta, + sample.versions, + run.meta, + run.versions + ).match() }, + { assert sample.majority_tsv != null }, + { assert sample.single_tsv != null }, + { assert sample.results != null }, + { assert run.csv != null }, + { assert run.results != null } + ) + } + } +} diff --git a/subworkflows/traitar/tests/main.nf.test.snap b/subworkflows/traitar/tests/main.nf.test.snap new file mode 100644 index 000000000..2fa921560 --- /dev/null +++ b/subworkflows/traitar/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "traitar - subworkflow - GCF_000017085": { + "content": [ + { + "id": "GCF_000017085-TRAITAR:TRAITAR_RUN", + "logs_dir": "GCF_000017085/tools/traitar//logs/", + "name": "GCF_000017085", + "output_dir": "GCF_000017085/tools/traitar/", + "process_name": "traitar", + "scope": "sample" + }, + [ + "versions.yml:md5,f25ec232bc89b44f8f431a04aee60879" + ], + { + "id": "traitar-majority-TRAITAR:CSVTK_CONCAT_MAJORITY", + "logs_dir": "merged-results/logs/traitar-majority-concat/", + "name": "traitar-majority", + "output_dir": "merged-results", + "process_name": "traitar-majority-concat", + "scope": "run" + }, + [ + "versions.yml:md5,0876b2d126e96f86b158fe8dddf4f05f" + ] + ], + "timestamp": "2026-05-06T08:40:48.418831853", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/traitar/tests/nextflow.config b/subworkflows/traitar/tests/nextflow.config new file mode 100644 index 000000000..c3e957589 --- /dev/null +++ b/subworkflows/traitar/tests/nextflow.config @@ -0,0 +1,41 @@ +// Minimal config for subworkflow-level testing of TRAITAR +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "traitar" + logo_name = "bactopia-tools" + description = "Predict phenotypic traits from microbial genomes" + ext = "fna" + } + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Load module configs for processes in this subworkflow +includeConfig "../../../modules/traitar/run/module.config" +includeConfig "../../../modules/traitar/download/module.config" +includeConfig "../../../modules/csvtk/concat/module.config" + +// Base config (container resolution + resource labels) +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" + +// Plugin +plugins { + id 'nf-bactopia@2.1.3' +} diff --git a/subworkflows/traitar/tests/nf-test.config b/subworkflows/traitar/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/subworkflows/traitar/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/workflows/bactopia-tools/traitar/main.nf b/workflows/bactopia-tools/traitar/main.nf new file mode 100644 index 000000000..961fe77f7 --- /dev/null +++ b/workflows/bactopia-tools/traitar/main.nf @@ -0,0 +1,91 @@ +#!/usr/bin/env nextflow +/** + * Predict phenotypic traits from microbial genomes + * + * This Bactopia Tool uses [Traitar](https://github.com/nick-youngblut/traitar3/) to predict phenotypic traits from microbial genomes. + * + * @status stable + * @keywords phenotype, traits, pfam, bactopia-tool + * @tags complexity:simple input-type:parameter output-type:multiple features:bactopia-tool,aggregation + * @citation csvtk, traitar + * + * @subworkflows utils_bactopia-tools, traitar + * + * @input rundir + * Directory containing results from a completed Bactopia analysis run + * + * @input traitar_db + * Path to a Pfam-A HMM file (optional) + * + * @input download_traitar + * Boolean flag to trigger automatic database download + * + * @section Per-Sample Results + * @publish *.majority.tsv Majority-vote combined phenotype trait predictions + * @publish *.single_votes.tsv Single-votes combined phenotype trait predictions + * @publish supplemental/* Supplemental Traitar output files + * + * @section Merged Results + * @publish traitar-majority.tsv Merged majority-vote phenotype predictions from all samples + * @publish traitar-single.tsv Merged single-vote phenotype predictions from all samples + * + * @section Execution Logs + * @publish logs/traitar/* Tool execution logs (stdout/stderr) + * @publish logs/nf-* Nextflow execution scripts and logs for debugging + * + * @section Versions + * @publish versions.yml Software version information + */ +nextflow.enable.types = true + +params { + rundir : String + + // Tool-specific parameters + traitar_db : Path? + download_traitar : Boolean +} + +include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' +include { TRAITAR } from '../../../subworkflows/traitar/main' +include { collectNextflowLogs } from 'plugin/nf-bactopia' + +workflow { + main: + ch_bactopiatool = BACTOPIATOOL_INIT() + ch_traitar = TRAITAR(ch_bactopiatool.assembly, params.traitar_db, params.download_traitar) + + publish: + // Per-sample + sample_outputs = ch_traitar.sample_outputs + sample_nf_logs = collectNextflowLogs(ch_traitar.sample_outputs) + // Run-level + run_outputs = ch_traitar.run_outputs + run_nf_logs = collectNextflowLogs(ch_traitar.run_outputs) +} + +output { + // Sample-level outputs (stored in ${params.outdir}//) + sample_outputs { + path { r -> + r.results.flatten() >> "${r.meta.output_dir}/" + r.logs.flatten() >> "${r.meta.logs_dir}/" + r.versions.flatten() >> "${r.meta.logs_dir}/" + } + } + sample_nf_logs { + path { meta, f -> f >> "${meta.logs_dir}/nf${f.name}" } + } + + // Run-level outputs (stored in ${params.outdir}/bactopia-runs//) + run_outputs { + path { r -> + r.results.flatten() >> "${params.rundir}/${r.meta.output_dir}/" + r.logs.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + r.versions.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + } + } + run_nf_logs { + path { meta, f -> f >> "${params.rundir}/${meta.logs_dir}/nf${f.name}" } + } +} diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config new file mode 100644 index 000000000..582311a34 --- /dev/null +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -0,0 +1,92 @@ +// main script name +manifest { + author = 'Robert A. Petit III' + name = 'bactopia' + homePage = 'https://github.com/bactopia/bactopia' + description = 'An extensive workflow for processing sequencing of bacterial genomes.' + mainScript = 'main.nf' + version = '4.0.1' + nextflowVersion = '>=26.04.0' +} + +params { + workflow { + name = "traitar" + logo_name = "bactopia-tools" + description = "Predict phenotypic traits from microbial genomes" + ext = ['fna'] + } +} + +// Version +params.bactopia_version = '4.0.1' +manifest.version = "${params.bactopia_version}" + +// Includes +params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +includeConfig "../../../conf/params.config" +includeConfig "../../../conf/params/bactopia-tools.config" + +// Module specific config +includeConfig "../../../modules/csvtk/concat/module.config" +includeConfig "../../../modules/traitar/download/module.config" +includeConfig "../../../modules/traitar/run/module.config" + +// Set output directory +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode +workflow.output.overwrite = params.force + +// Set up run directory +params.singularity_cache = env("NXF_SINGULARITY_CACHEDIR") ? "${env('NXF_SINGULARITY_CACHEDIR')}" : "${params.singularity_cache}" +params.run_timestamp = new java.util.Date().format('yyyyMMdd-HHmmss') +params.rundir = params.is_ci ? "bactopia-runs/${params.run_name}" : "bactopia-runs/${params.run_name}-${params.run_timestamp}" +params.infodir = "${params.outdir}/${params.rundir}/nf-reports" + +// Load nf-core custom profiles from different Institutions +includeConfig !env('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + +// Load Bactopia custom profiles from different institutions. +// Uncomment in the event a bactopia specific profile is added +//includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bactopia.config" : "/dev/null" + +// Base Config +includeConfig "../../../conf/base.config" + +// Profiles +includeConfig "../../../conf/profiles.config" + +// Reporting configuration +timeline { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-timeline.html" +} + +report { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-report.html" +} + +trace { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-trace.txt" + fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem' +} + +dag { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-dag.svg" +} + +// Plugins +plugins { + id 'nf-bactopia@2.1.3' +} + +bactopia { + parametersSchema = "${projectDir}/nextflow_schema.json" +} \ No newline at end of file diff --git a/workflows/bactopia-tools/traitar/nextflow_schema.json b/workflows/bactopia-tools/traitar/nextflow_schema.json new file mode 100644 index 000000000..3ff64cfce --- /dev/null +++ b/workflows/bactopia-tools/traitar/nextflow_schema.json @@ -0,0 +1,453 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/bactopia-tools.json", + "title": "traitar", + "description": "Predict phenotypic traits from microbial genomes", + "type": "object", + "$defs": { + "input_parameters": { + "title": "Required Parameters", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "help_text": "", + "properties": { + "bactopia": { + "type": "string", + "description": "The path to bactopia results to use as inputs", + "help": "The required inputs will be automatically selected by the subworkflow.", + "fa_icon": "fas fa-bacterium", + "header": "Bactopia Results" + } + } + }, + "filter_parameters": { + "title": "Filtering Parameters", + "type": "object", + "description": "Use these parameters to specify which samples to include or exclude.", + "default": "", + "fa_icon": "fa-solid fa-filter", + "properties": { + "include": { + "type": "string", + "description": "A text file containing sample names (one per line) to include from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-plus" + }, + "exclude": { + "type": "string", + "description": "A text file containing sample names (one per line) to exclude from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-minus" + } + } + }, + "traitar_download_parameters": { + "title": "Traitar Download Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "traitar_db": { + "type": "string", + "description": "Path to the Pfam-A HMM file for Traitar", + "fa_icon": "fas fa-font", + "is_required": true + }, + "download_traitar": { + "type": "boolean", + "description": "Download the Pfam database to the path given by --traitar_db", + "default": false, + "fa_icon": "fas fa-toggle-on" + } + } + }, + "csvtk_concat_parameters": { + "title": "csvtk concat Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "csvtk_concat_opts": { + "type": "string", + "description": "Extra csvtk concat options in quotes", + "help": "", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, + "optional_parameters": { + "title": "Optional Parameters", + "type": "object", + "description": "These optional parameters can be useful in certain settings.", + "default": "", + "fa_icon": "fa-solid fa-gears", + "properties": { + "outdir": { + "type": "string", + "default": "bactopia", + "description": "Base directory to write results to", + "fa_icon": "fas fa-folder" + }, + "skip_compression": { + "type": "boolean", + "default": false, + "description": "Output files will not be compressed", + "help": "Using this parameter can lead to a significant increase in the size of the outputs", + "fa_icon": "fas fa-expand-arrows-alt", + "hidden": true + }, + "datasets": { + "type": "string", + "fa_icon": "fas fa-folder", + "description": "The path to cache datasets to", + "hidden": true + }, + "keep_all_files": { + "type": "boolean", + "default": false, + "description": "Keeps all analysis files created", + "help": "By default, intermediate files are removed. This will not affect the ability to resume Nextflow runs, and only occurs at the end of the process.", + "fa_icon": "fas fa-trash-restore", + "hidden": true + } + } + }, + "max_job_request_parameters": { + "title": "Max Job Request Parameters", + "type": "object", + "fa_icon": "fa-solid fa-arrow-up-right-dots", + "description": "Set the top limit for requested resources for any single job.", + "hidden": true, + "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", + "properties": { + "max_retry": { + "type": "integer", + "description": "Maximum times to retry a process before allowing it to fail.", + "default": 3, + "fa_icon": "fas fa-redo", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of retry attempts for each process. Should be an integer e.g. `--max_retry 1`" + }, + "max_cpus": { + "type": "integer", + "description": "Maximum number of CPUs that can be requested for any single job.", + "default": 4, + "fa_icon": "fas fa-microchip", + "hidden": true, + "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" + }, + "max_memory": { + "type": "string", + "description": "Maximum amount of memory that can be requested for any single job.", + "default": "128.GB", + "fa_icon": "fas fa-memory", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "hidden": true, + "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" + }, + "max_time": { + "type": "string", + "description": "Maximum amount of time that can be requested for any single job.", + "default": "240.h", + "fa_icon": "far fa-clock", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", + "hidden": true, + "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '1.h'`" + }, + "max_downloads": { + "type": "integer", + "description": "Maximum number of samples to download at a time", + "default": 3, + "fa_icon": "fas fa-angle-double-up", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of downloads at a time" + } + } + }, + "nextflow_parameters": { + "title": "Nextflow Configuration Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-solid fa-screwdriver-wrench", + "properties": { + "nfconfig": { + "type": "string", + "description": "A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.", + "help": "This allows you to create profiles specific to your environment (e.g. SGE, AWS, SLURM, etc...).", + "fa_icon": "fas fa-cog", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "hidden": true, + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ] + }, + "infodir": { + "type": "string", + "description": "Directory to keep pipeline Nextflow logs and reports.", + "default": "${params.outdir}/pipeline_info", + "fa_icon": "fas fa-cogs", + "hidden": true + }, + "force": { + "type": "boolean", + "default": false, + "description": "Nextflow will overwrite existing output files.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "cleanup_workdir": { + "type": "boolean", + "default": false, + "description": "After Bactopia is successfully executed, the `work` directory will be deleted.", + "help": "Warning: by doing this you lose the ability to resume workflows.", + "fa_icon": "fas fa-trash-alt", + "hidden": true + } + } + }, + "institutional_config_options": { + "title": "Institutional config options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralized config profiles. These should not be edited.", + "help_text": "The centralized nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "properties": { + "custom_config_version": { + "type": "string", + "description": "Git commit id for Institutional configs.", + "default": "master", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "custom_config_base": { + "type": "string", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", + "hidden": true, + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" + }, + "config_profile_name": { + "type": "string", + "description": "Institutional config name.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_description": { + "type": "string", + "description": "Institutional config description.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_url": { + "type": "string", + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + } + } + }, + "nextflow_profile_parameters": { + "title": "Nextflow Profile Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-regular fa-address-card", + "properties": { + "condadir": { + "type": "string", + "description": "Directory to Nextflow should use for Conda environments", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "registry": { + "type": "string", + "default": "quay.io", + "hidden": true, + "description": "Registry to pull Docker containers from.", + "fa_icon": "fas fa-box" + }, + "datasets_cache": { + "type": "string", + "default": "/.bactopia/datasets", + "description": "Directory where downloaded datasets should be stored.", + "help": "", + "fa_icon": "fas fa-folder" + }, + "singularity_cache": { + "type": "string", + "description": "Directory where remote Singularity images are stored.", + "help": "If using a cluster, it must be accessible from all compute nodes. The NXF_SINGULARITY_CACHEDIR environment variable overrides this parameter", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.", + "hidden": true, + "fa_icon": "fas fa-toolbox", + "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues." + }, + "force_rebuild": { + "type": "boolean", + "default": false, + "description": "Force overwrite of existing pre-built environments.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "queue": { + "type": "string", + "default": "general,high-memory", + "description": "Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "cluster_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "container_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D `pwd`'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "disable_scratch": { + "type": "boolean", + "default": false, + "description": "All intermediate files created on worker nodes of will be transferred to the head node.", + "help": "Typically with clusters intermediate results are written to a 'scratch' space and only published result files are transferred back", + "fa_icon": "fas fa-toggle-off", + "hidden": true + } + } + }, + "generic_parameters": { + "title": "Helpful Parameters", + "type": "object", + "fa_icon": "fa-solid fa-reply-all", + "description": "Uncommonly used parameters that might be useful.", + "properties": { + "monochrome_logs": { + "type": "boolean", + "description": "Do not use coloured log outputs.", + "fa_icon": "fas fa-palette", + "hidden": true, + "help_text": "Set to disable colourful command line output and live life in monochrome." + }, + "nfdir": { + "type": "boolean", + "description": "Print directory Nextflow has pulled Bactopia to", + "fa_icon": "fas fa-remove-format", + "hidden": true + }, + "sleep_time": { + "type": "integer", + "description": "The amount of time (seconds) Nextflow will wait after setting up datasets before execution.", + "default": 5, + "fa_icon": "far fa-clock", + "hidden": true + }, + "validate_params": { + "type": "boolean", + "default": true, + "fa_icon": "fas fa-tasks", + "description": "Boolean whether to validate parameters against the schema at runtime", + "hidden": true + }, + "help": { + "type": "boolean", + "description": "Display help text.", + "hidden": true, + "fa_icon": "fas fa-question-circle" + }, + "wf": { + "type": "string", + "description": "Specify which workflow or Bactopia Tool to execute", + "default": "bactopia", + "fa_icon": "fas fa-bacteria" + }, + "list_wfs": { + "type": "boolean", + "description": "List the available workflows and Bactopia Tools to use with '--wf'", + "fa_icon": "fas fa-list" + }, + "show_hidden_params": { + "type": "boolean", + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters.", + "description": "Show all params when using `--help`", + "fa_icon": "far fa-eye", + "hidden": true + }, + "help_all": { + "type": "boolean", + "description": "An alias for --help --show_hidden_params", + "fa_icon": "fas fa-question-circle" + }, + "version": { + "type": "boolean", + "description": "Display version text.", + "fa_icon": "fas fa-info" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_parameters" + }, + { + "$ref": "#/$defs/filter_parameters" + }, + { + "$ref": "#/$defs/traitar_download_parameters" + }, + { + "$ref": "#/$defs/csvtk_concat_parameters" + }, + { + "$ref": "#/$defs/optional_parameters" + }, + { + "$ref": "#/$defs/max_job_request_parameters" + }, + { + "$ref": "#/$defs/nextflow_parameters" + }, + { + "$ref": "#/$defs/nextflow_profile_parameters" + }, + { + "$ref": "#/$defs/generic_parameters" + } + ] +} \ No newline at end of file diff --git a/workflows/bactopia-tools/traitar/tests/.nftignore b/workflows/bactopia-tools/traitar/tests/.nftignore new file mode 100644 index 000000000..17f86767b --- /dev/null +++ b/workflows/bactopia-tools/traitar/tests/.nftignore @@ -0,0 +1,5 @@ +**/*.{err,gz,html,log,pdf,stderr,stdout} +**/*.tsv +**/nf.command.* +**/supplemental/** +bactopia-runs/**/nf-reports/*.{dot,html} diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test b/workflows/bactopia-tools/traitar/tests/main.nf.test new file mode 100644 index 000000000..562888cd7 --- /dev/null +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_pipeline { + name "Test traitar Workflow" + script "../main.nf" + config "../../../../conf/test.config" + tag "workflows" + tag "bactopia-tools" + tag "traitar" + + test("traitar - GCF_000017085|staphylococcus_aureus|compressed_fasta") { + when { + params { + bactopia_test = "/species/staphylococcus_aureus/compressed" + test_dataset = "datasets/traitar" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap new file mode 100644 index 000000000..d597d693f --- /dev/null +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap @@ -0,0 +1,77 @@ +{ + "traitar - GCF_000017085|staphylococcus_aureus|compressed_fasta": { + "content": [ + 3, + [ + "GCF_000017085", + "GCF_000017085/tools", + "GCF_000017085/tools/traitar", + "GCF_000017085/tools/traitar/GCF_000017085.majority.tsv", + "GCF_000017085/tools/traitar/GCF_000017085.single_votes.tsv", + "GCF_000017085/tools/traitar/logs", + "GCF_000017085/tools/traitar/logs/nf.command.begin", + "GCF_000017085/tools/traitar/logs/nf.command.err", + "GCF_000017085/tools/traitar/logs/nf.command.log", + "GCF_000017085/tools/traitar/logs/nf.command.out", + "GCF_000017085/tools/traitar/logs/nf.command.run", + "GCF_000017085/tools/traitar/logs/nf.command.sh", + "GCF_000017085/tools/traitar/logs/nf.command.trace", + "GCF_000017085/tools/traitar/logs/versions.yml", + "GCF_000017085/tools/traitar/supplemental", + "GCF_000017085/tools/traitar/supplemental/annotation", + "GCF_000017085/tools/traitar/supplemental/annotation/pfam", + "GCF_000017085/tools/traitar/supplemental/annotation/pfam/GCF_000017085_domtblout.dat", + "GCF_000017085/tools/traitar/supplemental/annotation/pfam/GCF_000017085_filtered_best.dat", + "GCF_000017085/tools/traitar/supplemental/annotation/pfam/summary.dat", + "GCF_000017085/tools/traitar/supplemental/gene_prediction", + "GCF_000017085/tools/traitar/supplemental/gene_prediction/GCF_000017085.faa", + "GCF_000017085/tools/traitar/supplemental/gene_prediction/GCF_000017085.gff", + "GCF_000017085/tools/traitar/supplemental/phenotype_prediction", + "GCF_000017085/tools/traitar/supplemental/phenotype_prediction/predictions_flat_majority-votes_combined.txt", + "GCF_000017085/tools/traitar/supplemental/phenotype_prediction/predictions_flat_single-votes_combined.txt", + "GCF_000017085/tools/traitar/supplemental/predictions_conservative-vote.txt", + "GCF_000017085/tools/traitar/supplemental/predictions_majority-vote.txt", + "GCF_000017085/tools/traitar/supplemental/predictions_raw.txt", + "GCF_000017085/tools/traitar/supplemental/predictions_single-votes.txt", + "bactopia-runs", + "bactopia-runs/traitar", + "bactopia-runs/traitar/merged-results", + "bactopia-runs/traitar/merged-results/logs", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.begin", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.err", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.log", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.out", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.run", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.sh", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/nf.command.trace", + "bactopia-runs/traitar/merged-results/logs/traitar-majority-concat/versions.yml", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.begin", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.err", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.log", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.out", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.run", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.sh", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/nf.command.trace", + "bactopia-runs/traitar/merged-results/logs/traitar-single-concat/versions.yml", + "bactopia-runs/traitar/merged-results/traitar-majority.tsv", + "bactopia-runs/traitar/merged-results/traitar-single.tsv", + "bactopia-runs/traitar/nf-reports", + "bactopia-runs/traitar/nf-reports/traitar-dag.dot", + "bactopia-runs/traitar/nf-reports/traitar-report.html", + "bactopia-runs/traitar/nf-reports/traitar-timeline.html" + ], + [ + "versions.yml:md5,f25ec232bc89b44f8f431a04aee60879", + "versions.yml:md5,0876b2d126e96f86b158fe8dddf4f05f", + "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" + ] + ], + "timestamp": "2026-05-06T09:00:06.520660486", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/workflows/bactopia-tools/traitar/tests/nf-test.config b/workflows/bactopia-tools/traitar/tests/nf-test.config new file mode 100644 index 000000000..8f297479d --- /dev/null +++ b/workflows/bactopia-tools/traitar/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "../nextflow.config" + profile "" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} From 00e4b6c52052d54bde2b5e33fe81f4213e1d3fa9 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 09:16:18 -0600 Subject: [PATCH 07/43] update changelog --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9685f3e19..6175e4324 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,13 @@ sidebar_position: 5000 ## v4.0.1 bactopia/bactopia "???" 2026/??/?? +### `Added` + +- Bactopia Tools (`bactopia --wf `) + - `staphscan` - Genome-based surveillance analysis of _Staphylococcus aureus_ + - `traitar` - Predict phenotypic traits from microbial genomes +- Added StaphSCAN to the Staphtyper and Merlin subworkflows + ### `Fixed` - float parameters being interpreted as strings in CLI From c8b4383e14b96d074db8ea3e934feaeadf7dc890 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 10:07:09 -0600 Subject: [PATCH 08/43] bumpo plugin version --- catalog.json | 2 +- nextflow.config | 2 +- subworkflows/abricate/tests/nextflow.config | 2 +- subworkflows/abritamr/tests/nextflow.config | 2 +- subworkflows/agrvate/tests/nextflow.config | 2 +- subworkflows/amrfinderplus/tests/nextflow.config | 2 +- subworkflows/ariba/tests/nextflow.config | 2 +- subworkflows/bactopia/assembler/tests/nextflow.config | 2 +- subworkflows/bactopia/qc/tests/nextflow.config | 2 +- subworkflows/bactopia/sketcher/tests/nextflow.config | 2 +- subworkflows/bakta/tests/nextflow.config | 2 +- subworkflows/blastn/tests/nextflow.config | 2 +- subworkflows/blastp/tests/nextflow.config | 2 +- subworkflows/blastx/tests/nextflow.config | 2 +- subworkflows/bracken/tests/nextflow.config | 2 +- subworkflows/btyper3/tests/nextflow.config | 2 +- subworkflows/busco/tests/nextflow.config | 2 +- subworkflows/checkm/tests/nextflow.config | 2 +- subworkflows/checkm2/tests/nextflow.config | 2 +- subworkflows/clermontyping/tests/nextflow.config | 2 +- subworkflows/clonalframeml/tests/nextflow.config | 2 +- subworkflows/defensefinder/tests/nextflow.config | 2 +- subworkflows/ectyper/tests/nextflow.config | 2 +- subworkflows/eggnog/tests/nextflow.config | 2 +- subworkflows/emmtyper/tests/nextflow.config | 2 +- subworkflows/fastani/tests/nextflow.config | 2 +- subworkflows/gamma/tests/nextflow.config | 2 +- subworkflows/genotyphi/tests/nextflow.config | 2 +- subworkflows/gigatyper/tests/nextflow.config | 2 +- subworkflows/gtdb/tests/nextflow.config | 2 +- subworkflows/gubbins/tests/nextflow.config | 2 +- subworkflows/hicap/tests/nextflow.config | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 2 +- subworkflows/iqtree/tests/nextflow.config | 2 +- subworkflows/ismapper/tests/nextflow.config | 2 +- subworkflows/kleborate/tests/nextflow.config | 2 +- subworkflows/kraken2/tests/nextflow.config | 2 +- subworkflows/legsta/tests/nextflow.config | 2 +- subworkflows/lissero/tests/nextflow.config | 2 +- subworkflows/mashdist/tests/nextflow.config | 2 +- subworkflows/mashtree/tests/nextflow.config | 2 +- subworkflows/mcroni/tests/nextflow.config | 2 +- subworkflows/meningotype/tests/nextflow.config | 2 +- subworkflows/merlin/tests/nextflow.config | 2 +- subworkflows/merlindist/tests/nextflow.config | 2 +- subworkflows/midas/tests/nextflow.config | 2 +- subworkflows/mlst/tests/nextflow.config | 2 +- subworkflows/mobsuite/tests/nextflow.config | 2 +- subworkflows/mykrobe/tests/nextflow.config | 2 +- subworkflows/ncbigenomedownload/tests/nextflow.config | 2 +- subworkflows/ngmaster/tests/nextflow.config | 2 +- subworkflows/nohuman/tests/nextflow.config | 2 +- subworkflows/panaroo/tests/nextflow.config | 2 +- subworkflows/pangenome/tests/nextflow.config | 2 +- subworkflows/pasty/tests/nextflow.config | 2 +- subworkflows/pbptyper/tests/nextflow.config | 2 +- subworkflows/phispy/tests/nextflow.config | 2 +- subworkflows/pirate/tests/nextflow.config | 2 +- subworkflows/plasmidfinder/tests/nextflow.config | 2 +- subworkflows/pneumocat/tests/nextflow.config | 2 +- subworkflows/prokka/tests/nextflow.config | 2 +- subworkflows/quast/tests/nextflow.config | 2 +- subworkflows/rgi/tests/nextflow.config | 2 +- subworkflows/roary/tests/nextflow.config | 2 +- subworkflows/sccmec/tests/nextflow.config | 2 +- subworkflows/scoary/tests/nextflow.config | 2 +- subworkflows/scrubber/tests/nextflow.config | 2 +- subworkflows/seqsero2/tests/nextflow.config | 2 +- subworkflows/seroba/tests/nextflow.config | 2 +- subworkflows/shigapass/tests/nextflow.config | 2 +- subworkflows/shigatyper/tests/nextflow.config | 2 +- subworkflows/shigeifinder/tests/nextflow.config | 2 +- subworkflows/sistr/tests/nextflow.config | 2 +- subworkflows/snippy/core/tests/nextflow.config | 2 +- subworkflows/snippy/run/tests/nextflow.config | 2 +- subworkflows/snpdists/tests/nextflow.config | 2 +- subworkflows/spatyper/tests/nextflow.config | 2 +- subworkflows/srahumanscrubber/tests/nextflow.config | 2 +- subworkflows/ssuissero/tests/nextflow.config | 2 +- subworkflows/staphopiasccmec/tests/nextflow.config | 2 +- subworkflows/staphscan/tests/nextflow.config | 2 +- subworkflows/staphtyper/tests/nextflow.config | 2 +- subworkflows/stecfinder/tests/nextflow.config | 2 +- subworkflows/sylph/tests/nextflow.config | 2 +- subworkflows/tblastn/tests/nextflow.config | 2 +- subworkflows/tblastx/tests/nextflow.config | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 2 +- subworkflows/teton/tests/nextflow.config | 2 +- subworkflows/traitar/tests/nextflow.config | 2 +- workflows/bactopia-tools/abricate/nextflow.config | 2 +- workflows/bactopia-tools/abritamr/nextflow.config | 2 +- workflows/bactopia-tools/agrvate/nextflow.config | 2 +- workflows/bactopia-tools/amrfinderplus/nextflow.config | 2 +- workflows/bactopia-tools/ariba/nextflow.config | 2 +- workflows/bactopia-tools/bakta/nextflow.config | 2 +- workflows/bactopia-tools/blastn/nextflow.config | 2 +- workflows/bactopia-tools/blastp/nextflow.config | 2 +- workflows/bactopia-tools/blastx/nextflow.config | 2 +- workflows/bactopia-tools/bracken/nextflow.config | 2 +- workflows/bactopia-tools/btyper3/nextflow.config | 2 +- workflows/bactopia-tools/busco/nextflow.config | 2 +- workflows/bactopia-tools/checkm/nextflow.config | 2 +- workflows/bactopia-tools/checkm2/nextflow.config | 2 +- workflows/bactopia-tools/clermontyping/nextflow.config | 2 +- workflows/bactopia-tools/defensefinder/nextflow.config | 2 +- workflows/bactopia-tools/ectyper/nextflow.config | 2 +- workflows/bactopia-tools/eggnog/nextflow.config | 2 +- workflows/bactopia-tools/emmtyper/nextflow.config | 2 +- workflows/bactopia-tools/fastani/nextflow.config | 2 +- workflows/bactopia-tools/gamma/nextflow.config | 2 +- workflows/bactopia-tools/genotyphi/nextflow.config | 2 +- workflows/bactopia-tools/gigatyper/nextflow.config | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 2 +- workflows/bactopia-tools/hicap/nextflow.config | 2 +- workflows/bactopia-tools/hpsuissero/nextflow.config | 2 +- workflows/bactopia-tools/ismapper/nextflow.config | 2 +- workflows/bactopia-tools/kleborate/nextflow.config | 2 +- workflows/bactopia-tools/kraken2/nextflow.config | 2 +- workflows/bactopia-tools/legsta/nextflow.config | 2 +- workflows/bactopia-tools/lissero/nextflow.config | 2 +- workflows/bactopia-tools/mashdist/nextflow.config | 2 +- workflows/bactopia-tools/mashtree/nextflow.config | 2 +- workflows/bactopia-tools/mcroni/nextflow.config | 2 +- workflows/bactopia-tools/meningotype/nextflow.config | 2 +- workflows/bactopia-tools/merlin/nextflow.config | 2 +- workflows/bactopia-tools/midas/nextflow.config | 2 +- workflows/bactopia-tools/mlst/nextflow.config | 2 +- workflows/bactopia-tools/mobsuite/nextflow.config | 2 +- workflows/bactopia-tools/mykrobe/nextflow.config | 2 +- workflows/bactopia-tools/ngmaster/nextflow.config | 2 +- workflows/bactopia-tools/pangenome/nextflow.config | 2 +- workflows/bactopia-tools/pasty/nextflow.config | 2 +- workflows/bactopia-tools/pbptyper/nextflow.config | 2 +- workflows/bactopia-tools/phispy/nextflow.config | 2 +- workflows/bactopia-tools/plasmidfinder/nextflow.config | 2 +- workflows/bactopia-tools/pneumocat/nextflow.config | 2 +- workflows/bactopia-tools/prokka/nextflow.config | 2 +- workflows/bactopia-tools/quast/nextflow.config | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 2 +- workflows/bactopia-tools/sccmec/nextflow.config | 2 +- workflows/bactopia-tools/scrubber/nextflow.config | 2 +- workflows/bactopia-tools/seqsero2/nextflow.config | 2 +- workflows/bactopia-tools/seroba/nextflow.config | 2 +- workflows/bactopia-tools/shigapass/nextflow.config | 2 +- workflows/bactopia-tools/shigatyper/nextflow.config | 2 +- workflows/bactopia-tools/shigeifinder/nextflow.config | 2 +- workflows/bactopia-tools/sistr/nextflow.config | 2 +- workflows/bactopia-tools/snippy/nextflow.config | 2 +- workflows/bactopia-tools/spatyper/nextflow.config | 2 +- workflows/bactopia-tools/ssuissero/nextflow.config | 2 +- workflows/bactopia-tools/staphscan/nextflow.config | 2 +- workflows/bactopia-tools/staphtyper/nextflow.config | 2 +- workflows/bactopia-tools/stecfinder/nextflow.config | 2 +- workflows/bactopia-tools/sylph/nextflow.config | 2 +- workflows/bactopia-tools/tblastn/nextflow.config | 2 +- workflows/bactopia-tools/tblastx/nextflow.config | 2 +- workflows/bactopia-tools/tbprofiler/nextflow.config | 2 +- workflows/bactopia-tools/traitar/nextflow.config | 4 ++-- workflows/cleanyerreads/nextflow.config | 2 +- workflows/staphopia/nextflow.config | 2 +- workflows/teton/nextflow.config | 2 +- 161 files changed, 162 insertions(+), 162 deletions(-) diff --git a/catalog.json b/catalog.json index b5b0f831d..83867bb8b 100644 --- a/catalog.json +++ b/catalog.json @@ -3,7 +3,7 @@ "generated": "2026-05-06T14:51:44Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.1.6", - "nf_bactopia_version": "2.1.3", + "nf_bactopia_version": "2.1.4", "modules": { "abricate_run": { "description": "Mass screening of contigs for antimicrobial and virulence genes.", diff --git a/nextflow.config b/nextflow.config index bf201ff01..264ab2d82 100644 --- a/nextflow.config +++ b/nextflow.config @@ -118,7 +118,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index db0fd5742..91139faf3 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index 2587a5739..bd7f3d574 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index 34bd39493..4e733b30d 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index 8dcb5ea63..2d14a5184 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index da3bd4372..4b5aa17e6 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index b45f40e7f..80f53e66a 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -67,5 +67,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index 3cd9d2448..092b04ab6 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -73,5 +73,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index 9569170ae..be2bd89cf 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index 3c244c8b1..ba467c5b3 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index f46904a5f..8dd8ae098 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index b127830ab..6ef85fdb7 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index 8ba4fd744..cc4973238 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index 2faf2a18f..655db915e 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index 90e0b1111..505496a52 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index 0d6895014..8a403df12 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index b96ed6848..347c49d55 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index c02336b5f..a2a3e6b17 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index 099da2304..feeaaf8da 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index 7a8726e64..8dc11b2e7 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index 9b3140316..293573f8f 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index cdfe2f6f2..4e4c7111f 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index ac1e85693..7a2adf402 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index 28bab2202..b49815b72 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index 7993be709..0d393cf35 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index 40930c6d3..bd3daccee 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index 3f9ca61e2..565a25353 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index eec915931..cd9404752 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index 6d703e73e..29fb7db6d 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index 13aaaad7e..3af52e155 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index 2613405f5..155b2a027 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index 015e018db..e645970aa 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index 07cd5c506..0bd24a2b9 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index 5342b926b..d2fcbbea6 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index 884cae7cf..9c99d1226 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index d8ac1e946..1e3cf0496 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index 23152a892..ec4cb42d3 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index 6376926b8..a67a8a203 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index f9a07876f..2821ee9fe 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index 74301eeb4..323365011 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index 5ab5a616d..ac0f4c36a 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index a24fcfc35..79d30bc7e 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index 8d2de7898..654b42928 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -63,5 +63,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index 360d0e504..e74f889cf 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index b737504c2..1738381bb 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index bff9533eb..bce8bdfae 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index c72928095..a8a09e929 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index d4a850f33..699fc11fb 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config index 3dd7e2c5a..2cf558d76 100644 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ b/subworkflows/ncbigenomedownload/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index 3ce246e5e..9f579c331 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index 8f108cfc5..3068f6a45 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index 0ca9317b2..e4de2406d 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index 6599e1b0d..71ee10dc6 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index 50303b6b3..b32eced83 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index 5443f0ef9..3a04d38b2 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index 31d78636a..b1857a810 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index a74a1d24d..580b47d87 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index 2dc14b1f9..655317f7c 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index 87296e133..3510bee1d 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index 527cd1942..b08628c4d 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index b254fa002..c91bf8824 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index 93fdfa3f7..9f26b9b56 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index 4e06fdd9c..3afa08bec 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 23bd5d921..1ca62e440 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index 125183bf4..3d7805866 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index ef36d023a..9625d1afe 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -44,5 +44,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index 6c2c44e66..df2e7b024 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 37b0c80b1..3ec269020 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index 69c46dbca..2b7bc37a1 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index bb5fade2b..505d5582f 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index a7bdacb7f..2b4145053 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index 4374b82bc..7e52406af 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index a26c906d1..834ada652 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -39,5 +39,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index 89b6aa835..f317c41f5 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index f8cac4d81..5e01e9e4b 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index 31f4358e1..e8fa674fa 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index 23232a696..a5f6ff5d3 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index 20e680383..ee7e31b47 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index 4a5787e1c..d1b15d848 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/staphscan/tests/nextflow.config b/subworkflows/staphscan/tests/nextflow.config index bc566e5c0..43a008a0b 100644 --- a/subworkflows/staphscan/tests/nextflow.config +++ b/subworkflows/staphscan/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 4b65ac350..0c96eadde 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index 973e89a45..ee1ce74bb 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index 698ade699..a7193ad2b 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index f60f3ced7..ecec1d6c5 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index 69ee863c3..2a31dc2f0 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index 7685427ad..4b1d44ee5 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index 5a4a940a9..ba4b5747d 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -42,5 +42,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/subworkflows/traitar/tests/nextflow.config b/subworkflows/traitar/tests/nextflow.config index c3e957589..67649c816 100644 --- a/subworkflows/traitar/tests/nextflow.config +++ b/subworkflows/traitar/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index 386ab973c..35bf46b5d 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 64fd11cbc..aef8ea97b 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index 59879e6c1..02939f490 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index 21b141c2a..f351fba1e 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index 16a212fff..f8cce8180 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 407a7aa3a..26d7e8a00 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index c651544cd..dd202ec2f 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 27d058f86..4d455d00c 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 455b2c293..64f3ac375 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 27abf0dfc..9f6cb3693 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index 0fe6e4b56..b34f325ff 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index 88d5b1a72..548aa6f60 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index d2284a32b..0e019cb1a 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 953c7156a..567c3dffc 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index ad1821f2e..528e9a12b 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index abeaffb5d..05d188ea7 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 978a54aa0..57a54e004 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index d43289951..0cf0e4ed7 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index fed4f3bdc..9e29ea10f 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index da03ae80f..ac1f67c50 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index cffab56f3..daf219628 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index 5b9986635..c6f604bd6 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index 4cbbb75d6..14730fb42 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index 39ca847c3..ed6e22b79 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index b882d16aa..97b528093 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index e5e6416d8..753c5d750 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 2244f1bab..63a4aa00d 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index fc86cab21..aad4766d5 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index a745b1610..3944eb428 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 0ac376101..13beac617 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index 50b367ed8..c0f74dfcb 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index 3b630fbf8..ae161e24a 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 05f14daee..7168892fe 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 11a4f1503..bdd6c5ed4 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index db72912f1..aa2e0359a 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index d76a05693..7e10bdbf7 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -111,7 +111,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index cbf1a09fc..5b8b24bbd 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index d1c338dfc..fd7d513fa 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index 75c39e24b..78deafdce 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index 7f39a41bf..f3027b08a 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 7f1b190fb..781b9b147 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index 02d08b735..f545cf08e 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index bd300c69d..1231f73f5 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index 6352ef33b..60155a7b5 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index da2500034..55c84a89c 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 9bd7be7ff..c19255968 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index 3c9d97f37..fa0acafa9 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index ee4c3c346..dfb2226f5 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 3109a2c19..7db17a2be 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index 6c6caf404..4b3dc8b25 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index 6c2a99e82..774bbdd34 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index ef541fd3e..ca107aea5 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index da3b5c530..aef16337b 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index 26a32aa8e..1a6d53456 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index c81fa9a48..2ccb59552 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 140815fda..2015cf435 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index c12ea87d8..9a078f9b8 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index 021712e8a..7fc974733 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 9d0564501..73f5ae3a8 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index ff362ddef..97cd8ccc9 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 51023c783..bcd48c8d6 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index 945068486..7a33dad20 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index fe9665dbd..36359167b 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index d9f181c98..741a0d361 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index bbe1cb21e..e9254b0f1 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index 1963b2c35..f68946d8c 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index e5591d523..ba20328fa 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 7e481d2ba..9e4ebf1a5 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index 582311a34..0b40bb3e4 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -84,9 +84,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index 48b90318e..e05f06dd5 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index bf6161722..6d18a57d9 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -98,7 +98,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 4f9f8bfdd..484012780 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -92,7 +92,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.3' + id 'nf-bactopia@2.1.4' } bactopia { From 9c8545d4a0bd586c9e66bbab8199867309661735 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 10:25:09 -0600 Subject: [PATCH 09/43] tweaks to traitar --- modules/traitar/download/module.config | 1 - modules/traitar/download/schema.json | 2 +- modules/traitar/run/main.nf | 3 +++ workflows/bactopia-tools/traitar/nextflow_schema.json | 7 +++---- 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/modules/traitar/download/module.config b/modules/traitar/download/module.config index 3ea704c9c..5d9a75b74 100644 --- a/modules/traitar/download/module.config +++ b/modules/traitar/download/module.config @@ -1,7 +1,6 @@ params { // traitar_download download_traitar = false - traitar_db = "" } process { diff --git a/modules/traitar/download/schema.json b/modules/traitar/download/schema.json index 72d94b49b..fdc687ddb 100644 --- a/modules/traitar/download/schema.json +++ b/modules/traitar/download/schema.json @@ -14,7 +14,7 @@ "properties": { "traitar_db": { "type": "string", - "description": "Path to the Pfam-A HMM file for Traitar", + "description": "Path a Traitar database (should contain the Pfam-A.hmm file)", "fa_icon": "fas fa-font", "is_required": true }, diff --git a/modules/traitar/run/main.nf b/modules/traitar/run/main.nf index 33907d103..50e27250d 100644 --- a/modules/traitar/run/main.nf +++ b/modules/traitar/run/main.nf @@ -40,6 +40,9 @@ process TRAITAR_RUN { ) db: Path + stage: + stageAs db, 'staging/db/*' + output: record( // Named fields (used downstream) diff --git a/workflows/bactopia-tools/traitar/nextflow_schema.json b/workflows/bactopia-tools/traitar/nextflow_schema.json index 3ff64cfce..d5a98c57c 100644 --- a/workflows/bactopia-tools/traitar/nextflow_schema.json +++ b/workflows/bactopia-tools/traitar/nextflow_schema.json @@ -51,9 +51,8 @@ "properties": { "traitar_db": { "type": "string", - "description": "Path to the Pfam-A HMM file for Traitar", - "fa_icon": "fas fa-font", - "is_required": true + "description": "Path a Traitar database (should contain the Pfam-A.hmm file)", + "fa_icon": "fas fa-font" }, "download_traitar": { "type": "boolean", @@ -450,4 +449,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} \ No newline at end of file +} From 8619b8ffe37daa4e0a09a624870415ae8e79f7ae Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 15:54:51 -0600 Subject: [PATCH 10/43] add deacon and set as default for scrubber --- CHANGELOG.md | 10 + catalog.json | 167 ++++++++++++- conf/params/teton.config | 2 +- conf/test.config | 2 + data/citations.yml | 7 + llms.txt | 2 +- modules/bactopia/teton/module.config | 6 +- modules/bracken/module.config | 6 +- modules/deacon/fetch/main.nf | 59 +++++ modules/deacon/fetch/module.config | 30 +++ modules/deacon/fetch/schema.json | 41 ++++ modules/deacon/filter/main.nf | 158 ++++++++++++ modules/deacon/filter/module.config | 33 +++ modules/deacon/filter/schema.json | 59 +++++ modules/deacon/filter/tests/main.nf.test | 123 ++++++++++ modules/deacon/filter/tests/main.nf.test.snap | 80 +++++++ modules/deacon/filter/tests/nextflow.config | 36 +++ modules/deacon/filter/tests/nf-test.config | 11 + modules/deacon/index/main.nf | 69 ++++++ modules/deacon/index/module.config | 23 ++ modules/deacon/index/schema.json | 29 +++ modules/kraken2/module.config | 6 +- modules/nohuman/download/module.config | 7 +- modules/nohuman/run/module.config | 6 +- modules/srahumanscrubber/scrub/module.config | 6 +- subworkflows/deacon/main.nf | 63 +++++ subworkflows/deacon/tests/main.nf.test | 44 ++++ subworkflows/deacon/tests/main.nf.test.snap | 24 ++ subworkflows/deacon/tests/nextflow.config | 40 ++++ subworkflows/deacon/tests/nf-test.config | 11 + subworkflows/scrubber/main.nf | 35 ++- subworkflows/scrubber/tests/main.nf.test | 58 ++++- subworkflows/scrubber/tests/nextflow.config | 2 + subworkflows/teton/main.nf | 25 +- workflows/bactopia-tools/scrubber/main.nf | 31 ++- .../bactopia-tools/scrubber/nextflow.config | 4 +- .../scrubber/nextflow_schema.json | 80 ++++++- .../bactopia-tools/scrubber/tests/.nftignore | 2 +- .../scrubber/tests/main.nf.test | 39 ++- .../scrubber/tests/main.nf.test.snap | 58 ++++- workflows/cleanyerreads/main.nf | 24 +- workflows/cleanyerreads/nextflow.config | 4 +- workflows/cleanyerreads/nextflow_schema.json | 87 +++++++ .../cleanyerreads/tests/main.nf.test.snap | 4 +- workflows/teton/main.nf | 26 +- workflows/teton/nextflow.config | 4 +- workflows/teton/nextflow_schema.json | 87 +++++++ workflows/teton/tests/main.nf.test | 42 +++- workflows/teton/tests/main.nf.test.snap | 224 ++++++++++++++++-- 49 files changed, 1905 insertions(+), 91 deletions(-) create mode 100644 modules/deacon/fetch/main.nf create mode 100644 modules/deacon/fetch/module.config create mode 100644 modules/deacon/fetch/schema.json create mode 100644 modules/deacon/filter/main.nf create mode 100644 modules/deacon/filter/module.config create mode 100644 modules/deacon/filter/schema.json create mode 100644 modules/deacon/filter/tests/main.nf.test create mode 100644 modules/deacon/filter/tests/main.nf.test.snap create mode 100644 modules/deacon/filter/tests/nextflow.config create mode 100644 modules/deacon/filter/tests/nf-test.config create mode 100644 modules/deacon/index/main.nf create mode 100644 modules/deacon/index/module.config create mode 100644 modules/deacon/index/schema.json create mode 100644 subworkflows/deacon/main.nf create mode 100644 subworkflows/deacon/tests/main.nf.test create mode 100644 subworkflows/deacon/tests/main.nf.test.snap create mode 100644 subworkflows/deacon/tests/nextflow.config create mode 100644 subworkflows/deacon/tests/nf-test.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 6175e4324..39b4272a1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,16 @@ sidebar_position: 5000 - `staphscan` - Genome-based surveillance analysis of _Staphylococcus aureus_ - `traitar` - Predict phenotypic traits from microbial genomes - Added StaphSCAN to the Staphtyper and Merlin subworkflows +- Deacon as the default host read scrubber (replaces nohuman as default) +- Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules +- Three-way scrubber selection: deacon (default), nohuman (`--use_nohuman`), SRA Human Scrubber (`--use_srascrubber`) + +### `Changed` + +- Updated bactopia-teton meta-package from 1.1.3 to 1.1.4 (includes deacon) +- Deacon modules now use bactopia-teton container instead of standalone deacon container +- Teton and scrubber workflows default to deacon instead of nohuman for host read removal +- cleanyerreads workflow supports `--use_deacon` flag for host read removal ### `Fixed` diff --git a/catalog.json b/catalog.json index 83867bb8b..5a0cb754d 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-05-06T14:51:44Z", + "generated": "2026-05-06T20:36:40Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.1.6", "nf_bactopia_version": "2.1.4", @@ -423,7 +423,7 @@ "process_name": "teton-prepare", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "takes": [ "classification" @@ -634,7 +634,7 @@ "process_name": "bracken", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "takes": [ "r1", @@ -905,6 +905,95 @@ ] } }, + "deacon_fetch": { + "description": "Fetch a pre-built deacon index for host read filtering.", + "path": "modules/deacon/fetch/", + "scope": "run", + "process_name": "deacon_fetch", + "tool": { + "name": "bactopia-teton", + "version": "1.1.4" + }, + "emits": [ + "db" + ], + "tags": { + "complexity": "simple", + "input_type": "none", + "output_type": "single", + "features": [ + "internet-access", + "resource-download", + "no-test" + ] + } + }, + "deacon_filter": { + "description": "Filter host reads from sequencing data using minimizer-based comparison.", + "path": "modules/deacon/filter/", + "scope": "sample", + "process_name": "deacon", + "tool": { + "name": "bactopia-teton", + "version": "1.1.4" + }, + "takes": [ + "r1", + "r2", + "se", + "lr" + ], + "takes_optional": [ + "r1", + "r2", + "se", + "lr" + ], + "emits": [ + "special_meta", + "r1", + "r2", + "se", + "lr", + "scrub_report" + ], + "emits_optional": [ + "r1", + "r2", + "se", + "lr" + ], + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "database-dependent", + "conditional-logic" + ] + } + }, + "deacon_index": { + "description": "Build a deacon minimizer index from a FASTA reference genome.", + "path": "modules/deacon/index/", + "scope": "run", + "process_name": "deacon_index", + "tool": { + "name": "bactopia-teton", + "version": "1.1.4" + }, + "emits": [ + "db" + ], + "tags": { + "complexity": "simple", + "input_type": "single", + "output_type": "single", + "features": [ + "no-test" + ] + } + }, "defensefinder_run": { "description": "Detect anti-phage defense systems using HMM profiles.", "path": "modules/defensefinder/run/", @@ -1396,7 +1485,7 @@ "process_name": "kraken2", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "takes": [ "r1", @@ -1888,7 +1977,7 @@ "process_name": "nohuman_download", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "emits": [ "db", @@ -1914,7 +2003,7 @@ "process_name": "nohuman", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "takes": [ "r1", @@ -2681,7 +2770,7 @@ "process_name": "srahumanscrubber", "tool": { "name": "bactopia-teton", - "version": "1.1.3" + "version": "1.1.4" }, "takes": [ "r1", @@ -3786,6 +3875,54 @@ ] } }, + "deacon": { + "description": "Remove host reads from sequencing data using deacon.", + "path": "subworkflows/deacon/", + "takes": [ + "r1", + "r2", + "se", + "lr" + ], + "takes_optional": [ + "r1", + "r2", + "se", + "lr" + ], + "takes_params": [ + "database", + "download_deacon" + ], + "emits": { + "sample_outputs": [ + "special_meta", + "r1", + "r2", + "se", + "lr", + "scrub_report" + ], + "run_outputs": [] + }, + "scope": "sample", + "calls": { + "modules": [ + "deacon_fetch", + "deacon_filter" + ] + }, + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "single", + "features": [ + "database-dependent", + "conditional-logic", + "resource-download" + ] + } + }, "defensefinder": { "description": "Systematically search for anti-phage defense systems.", "path": "subworkflows/defensefinder/", @@ -5439,9 +5576,12 @@ ], "takes_params": [ "use_srascrubber", + "use_nohuman", "nohuman_db", "download_nohuman", - "nohuman_save_as_tarball" + "nohuman_save_as_tarball", + "deacon_db", + "download_deacon" ], "emits": { "sample_outputs": [ @@ -5480,7 +5620,8 @@ ], "subworkflows": [ "srahumanscrubber", - "nohuman" + "nohuman", + "deacon" ] }, "tags": { @@ -6241,7 +6382,13 @@ ], "takes_params": [ "db", - "use_srascrubber" + "use_srascrubber", + "use_nohuman", + "nohuman_db", + "download_nohuman", + "nohuman_save_as_tarball", + "deacon_db", + "download_deacon" ], "emits": { "sample_outputs": [], diff --git a/conf/params/teton.config b/conf/params/teton.config index 94c8e613b..82fe0adfb 100644 --- a/conf/params/teton.config +++ b/conf/params/teton.config @@ -21,5 +21,5 @@ params { skip_scrubber = false // Params to ignore - schema_ignore_params = "${params.schema_ignore_params},bactopia,use_bakta,sampleseed,skip_scrubber,skip_fastq_check,ask_merlin,species,datasets,reassemble,assembly,short_polish,hybrid,available_datasets,use_nohuman" + schema_ignore_params = "${params.schema_ignore_params},bactopia,use_bakta,sampleseed,skip_scrubber,skip_fastq_check,ask_merlin,species,datasets,reassemble,assembly,short_polish,hybrid,available_datasets,use_nohuman,use_deacon" } diff --git a/conf/test.config b/conf/test.config index b3aab0cec..4484ad00b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -13,6 +13,7 @@ params { test_ont = null gamma_test = null nohuman_test = null + deacon_test = null is_ci = true max_retry = 1 @@ -46,6 +47,7 @@ params { midas_db = "${params.test_data_dir}/${params.test_dataset}" mlst_db = params.test_dataset ? "${params.test_data_dir}/${params.test_dataset}" : null mykrobe_species = params.test_dataset2 + deacon_db = params.deacon_test ? "${params.test_data_dir}/${params.deacon_test}" : null nohuman_db = params.nohuman_test ? "${params.test_data_dir}/${params.nohuman_test}" : null reference = "${params.test_data_dir}/${params.test_dataset2}" scoary_traits = params.test_dataset ? "${params.test_data_dir}/${params.test_dataset}" : null diff --git a/data/citations.yml b/data/citations.yml index c56927566..843bf251c 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -317,6 +317,13 @@ tools: cite: | Shen, W [csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang.](https://github.com/shenwei356/csvtk/) (GitHub) + deacon: + name: deacon + link: https://github.com/bede/deacon + description: SIMD-accelerated filtering of DNA sequences using minimizer-based comparison + cite: | + Bede N. [deacon: SIMD-accelerated filtering of DNA sequences using minimizer-based comparison.](https://github.com/bede/deacon) (GitHub) + defensefinder: name: DefenseFinder link: https://github.com/mdmparis/defense-finder diff --git a/llms.txt b/llms.txt index b7df9cbf5..a5dd7bba8 100644 --- a/llms.txt +++ b/llms.txt @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -101 tool-specific modules live under `modules/`. Each module directory contains: +104 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/bactopia/teton/module.config b/modules/bactopia/teton/module.config index 0499e2aa1..ce51f9b3e 100644 --- a/modules/bactopia/teton/module.config +++ b/modules/bactopia/teton/module.config @@ -14,9 +14,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/bracken/module.config b/modules/bracken/module.config index 34d429106..e84347916 100644 --- a/modules/bracken/module.config +++ b/modules/bracken/module.config @@ -47,9 +47,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/deacon/fetch/main.nf b/modules/deacon/fetch/main.nf new file mode 100644 index 000000000..e91c4f5c6 --- /dev/null +++ b/modules/deacon/fetch/main.nf @@ -0,0 +1,59 @@ +/** + * Fetch a pre-built deacon index for host read filtering. + * + * Uses [deacon](https://github.com/bede/deacon) to download a pre-built minimizer index + * for filtering host reads from sequencing data. The default index is `panhuman-1`, which + * covers human reference genomes for human read depletion. + * + * @status stable + * @keywords host, decontamination, depletion, download, index, minimizer, deacon + * @tags complexity:simple input-type:none output-type:single features:internet-access,resource-download,no-test + * @citation deacon + * + * @note Internet Required + * This process requires an active internet connection to fetch the pre-built index. + * + * @output record(db, logs) + * - `db`: The pre-built deacon minimizer index file + */ +nextflow.enable.types = true + +// bactopia-lint: ignore M012,M017,M018,M022,M023,M024,M025,M026,M028 +process DEACON_FETCH { + label 'process_single' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + output: + record( + db: file("${prefix}/${task.ext.deacon_index_name}.idx"), + logs: files("${prefix}/logs/*", optional: true) + ) + + script: + prefix = task.ext.process_name + """ + mkdir -p ${prefix}/logs + + deacon \\ + index \\ + fetch \\ + ${task.ext.deacon_index_name} \\ + > ${prefix}/${task.ext.deacon_index_name}.idx + + # Move outputs to tool specific folder + cp .command.begin ${prefix}/logs/nf.command.begin + cp .command.err ${prefix}/logs/nf.command.err + cp .command.log ${prefix}/logs/nf.command.log + cp .command.out ${prefix}/logs/nf.command.out + cp .command.run ${prefix}/logs/nf.command.run + cp .command.sh ${prefix}/logs/nf.command.sh + cp .command.trace ${prefix}/logs/nf.command.trace + + cat <<-END_VERSIONS > ${prefix}/logs/versions.yml + "${task.process}": + deacon: \$( deacon --version | head -n1 | sed 's/deacon //' ) + END_VERSIONS + """ +} diff --git a/modules/deacon/fetch/module.config b/modules/deacon/fetch/module.config new file mode 100644 index 000000000..e22861783 --- /dev/null +++ b/modules/deacon/fetch/module.config @@ -0,0 +1,30 @@ +params { + // deacon_fetch + deacon_index_name = "panhuman-1" + deacon_db = null + download_deacon = false + use_deacon = false +} + +process { + withName: 'DEACON_FETCH' { + ext.wf = params.wf + ext.scope = "run" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "deacon_fetch" + storeDir = params.datasets_cache + + // Tool arguments + ext.args = "" + + // Environment information + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" + ext.condaDir = "${params.condadir}" + + // Module-specific parameters + ext.deacon_index_name = params.deacon_index_name + } +} diff --git a/modules/deacon/fetch/schema.json b/modules/deacon/fetch/schema.json new file mode 100644 index 000000000..934e3d3e7 --- /dev/null +++ b/modules/deacon/fetch/schema.json @@ -0,0 +1,41 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/deacon/fetch/schema.json", + "title": "Deacon Fetch Module", + "description": "A module for fetching a pre-built deacon index for host read filtering", + "type": "object", + "$defs": { + "deacon_fetch_parameters": { + "title": "Deacon Fetch Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_index_name": { + "type": "string", + "default": "panhuman-1", + "description": "Name of the pre-built deacon index to fetch", + "fa_icon": "fas fa-font" + }, + "download_deacon": { + "type": "boolean", + "default": false, + "description": "Download the deacon index to the datasets cache", + "fa_icon": "fas fa-toggle-on" + }, + "use_deacon": { + "type": "boolean", + "default": false, + "description": "Use deacon for host read filtering", + "fa_icon": "fas fa-toggle-on" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/deacon_fetch_parameters" + } + ] +} diff --git a/modules/deacon/filter/main.nf b/modules/deacon/filter/main.nf new file mode 100644 index 000000000..2c64148bf --- /dev/null +++ b/modules/deacon/filter/main.nf @@ -0,0 +1,158 @@ +/** + * Filter host reads from sequencing data using minimizer-based comparison. + * + * Uses [deacon](https://github.com/bede/deacon) to identify and remove host reads from + * FASTQ files using SIMD-accelerated minimizer comparison against a pre-built or custom + * reference index. Supports paired-end, single-end, and long reads. + * + * @status stable + * @keywords host, contamination, decontamination, depletion, filtering, minimizer, reads, deacon + * @tags complexity:moderate input-type:single output-type:multiple features:database-dependent,conditional-logic + * @citation deacon + * + * @note Database Required + * Requires a deacon minimizer index. Use the deacon/fetch module to download a pre-built + * index (e.g., panhuman-1) or deacon/index to build one from a reference FASTA. + * + * @input record(meta, r1?, r2?, se?, lr?) + * - `meta`: Groovy Record containing sample information + * - `r1?`: Illumina R1 reads (paired-end forward) + * - `r2?`: Illumina R2 reads (paired-end reverse) + * - `se?`: Single-end Illumina reads + * - `lr?`: Long reads (ONT/PacBio) + * + * @input db + * Deacon minimizer index file (.idx) for host read filtering + * + * @output record(meta, special_meta, r1?, r2?, se?, lr?, scrub_report, results, logs, nf_logs, versions) + * - `special_meta`: A simplified metadata record for downstream report joining + * - `r1?`: Filtered paired-end forward reads + * - `r2?`: Filtered paired-end reverse reads + * - `se?`: Filtered single-end reads + * - `lr?`: Filtered long reads + * - `scrub_report`: Summary report of reads removed during filtering + */ +nextflow.enable.types = true + +process DEACON_FILTER { + tag "${prefix}" + label 'process_low' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + record ( + meta: Record, + r1: Path?, + r2: Path?, + se: Path?, + lr: Path? + ) + db: Path + + output: + record( + // Named fields (used downstream) + meta: meta, + special_meta: special_meta, + r1: file("${prefix}_R1.scrubbed.fastq.gz", optional: true), + r2: file("${prefix}_R2.scrubbed.fastq.gz", optional: true), + se: file("${prefix}.scrubbed.fastq.gz", optional: true), + lr: file("${prefix}.scrubbed.fastq.gz", optional: true), + scrub_report: file("${prefix}.scrub.report.tsv"), + json_summary: file("${prefix}.deacon.json"), + // Generic fields (used for publishing) + results: [ + files("${prefix}*.scrubbed.fastq.gz"), + files("${prefix}.scrub.report.tsv"), + files("${prefix}.deacon.json") + ], + logs: files("*.{log,err}", optional: true), + nf_logs: files(".command.*"), + versions: files("versions.yml") + ) + + script: + def _meta = meta + prefix = task.ext.prefix ?: "${_meta.name}" + output_folder = task.ext.wf == "scrubber" || task.ext.wf == "teton" ? "scrubber" : "${task.ext.process_name}" + + // Determine read type from explicit slots + has_r1 = r1 != null + has_r2 = r2 != null + has_se = se != null + has_lr = lr != null + + // Create a new meta variable + meta = record( + id: "${prefix}-${task.process}", + name: prefix, + scope: task.ext.scope, + output_dir: "${prefix}/tools/${output_folder}", + logs_dir: "${prefix}/tools/${output_folder}/logs/${task.ext.logs_subdir}", + process_name: task.ext.process_name, + single_end: (has_se || has_lr) && !has_r1 && !has_r2, + runtype: _meta.runtype != null ? _meta.runtype : (has_r1 && has_r2 ? "paired-end" : (has_lr ? "lr" : "se")) + ) + + // Simplified meta for downstream report joining + special_meta = record( + name: prefix + ) + + // Pick the single-file input (se or lr) + def single_reads = has_se ? "${se}" : "${lr}" + if (meta.single_end) { + """ + deacon \\ + filter \\ + --threads ${task.cpus} \\ + --summary ${prefix}.deacon.json \\ + ${task.ext.args} \\ + ${db} \\ + ${single_reads} \\ + -o ${prefix}.scrubbed.fastq.gz + + # Quick stats on reads + zcat ${single_reads} | fastq-scan > original.json + zcat *.scrubbed.fastq.gz | fastq-scan > scrubbed.json + bactopia-scrubber-summary ${prefix} original.json scrubbed.json > ${prefix}.scrub.report.tsv + + # Cleanup + rm original.json scrubbed.json + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deacon: \$( deacon --version | head -n1 | sed 's/deacon //' ) + fastq-scan: \$(echo \$(fastq-scan -v 2>&1) | sed 's/fastq-scan //') + END_VERSIONS + """ + } else { + """ + deacon \\ + filter \\ + --threads ${task.cpus} \\ + --summary ${prefix}.deacon.json \\ + ${task.ext.args} \\ + ${db} \\ + ${r1} ${r2} \\ + -o ${prefix}_R1.scrubbed.fastq.gz \\ + -O ${prefix}_R2.scrubbed.fastq.gz + + # Quick stats on reads + zcat ${r1} ${r2} | fastq-scan > original.json + zcat *.scrubbed.fastq.gz | fastq-scan > scrubbed.json + bactopia-scrubber-summary ${prefix} original.json scrubbed.json > ${prefix}.scrub.report.tsv + + # Cleanup + rm original.json scrubbed.json + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deacon: \$( deacon --version | head -n1 | sed 's/deacon //' ) + fastq-scan: \$(echo \$(fastq-scan -v 2>&1) | sed 's/fastq-scan //') + END_VERSIONS + """ + } +} diff --git a/modules/deacon/filter/module.config b/modules/deacon/filter/module.config new file mode 100644 index 000000000..e5b5a624b --- /dev/null +++ b/modules/deacon/filter/module.config @@ -0,0 +1,33 @@ +params { + // deacon_filter + deacon_abs_threshold = 2 + deacon_deplete = true + deacon_opts = "" + deacon_prefix_length = 0 + deacon_rel_threshold = 0.01 +} + +process { + withName: 'DEACON_FILTER' { + ext.wf = params.wf + ext.scope = "sample" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "deacon" + + // Tool arguments + ext.args = [ + params.deacon_deplete ? "-d" : "", + params.deacon_abs_threshold != 2 ? "-a ${params.deacon_abs_threshold}" : "", + params.deacon_rel_threshold != 0.01 ? "-r ${params.deacon_rel_threshold}" : "", + params.deacon_prefix_length > 0 ? "-p ${params.deacon_prefix_length}" : "", + params.deacon_opts ? "${params.deacon_opts}" : "" + ].join(' ').replaceAll("\\s{2,}", " ").trim() + + // Environment information + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/deacon/filter/schema.json b/modules/deacon/filter/schema.json new file mode 100644 index 000000000..0604b7b9a --- /dev/null +++ b/modules/deacon/filter/schema.json @@ -0,0 +1,59 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/deacon/filter/schema.json", + "title": "Deacon Filter Module", + "description": "A module for filtering host reads from sequencing data using minimizer-based comparison", + "type": "object", + "$defs": { + "deacon_filter_parameters": { + "title": "Deacon Filter Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_abs_threshold": { + "type": "integer", + "default": 2, + "description": "Minimum absolute number of minimizer hits for a match", + "fa_icon": "fas fa-hashtag" + }, + "deacon_db": { + "type": "string", + "default": "", + "description": "Path to a pre-existing deacon index (.idx) for host read filtering", + "fa_icon": "fas fa-font" + }, + "deacon_deplete": { + "type": "boolean", + "default": true, + "description": "Discard matching sequences instead of keeping them", + "fa_icon": "fas fa-toggle-on" + }, + "deacon_opts": { + "type": "string", + "default": "", + "description": "Additional deacon filter options not covered by other parameters", + "fa_icon": "fas fa-font" + }, + "deacon_prefix_length": { + "type": "integer", + "default": 0, + "description": "Search only the first N nucleotides per sequence (0 for all)", + "fa_icon": "fas fa-hashtag" + }, + "deacon_rel_threshold": { + "type": "number", + "default": 0.01, + "description": "Minimum relative proportion (0.0-1.0) of minimizer hits for a match", + "fa_icon": "fas fa-percentage" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/deacon_filter_parameters" + } + ] +} diff --git a/modules/deacon/filter/tests/main.nf.test b/modules/deacon/filter/tests/main.nf.test new file mode 100644 index 000000000..3e12ad2c6 --- /dev/null +++ b/modules/deacon/filter/tests/main.nf.test @@ -0,0 +1,123 @@ +nextflow_process { + name "Test DEACON_FILTER" + script "../main.nf" + process "DEACON_FILTER" + tag "modules" + tag "deacon" + tag "deacon_filter" + + test("deacon_filter - module - SRR2838702 - PE") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "SRR2838702"], + r1: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R1.fastq.gz"), + r2: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R2.fastq.gz"), + se: null, + lr: null + ) + ) + input[1] = file("${params.test_data_dir}/datasets/deacon/panhuman-1.idx") + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert record.r1 != null }, + { assert record.r2 != null }, + { assert record.scrub_report != null }, + { assert record.special_meta != null }, + { assert snapshot( + record.meta, + record.special_meta, + record.scrub_report, + record.versions + ).match() } + ) + } + } + + test("deacon_filter - module - SRR2838702 - SE") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "SRR2838702"], + r1: null, + r2: null, + se: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702SE.fastq.gz"), + lr: null + ) + ) + input[1] = file("${params.test_data_dir}/datasets/deacon/panhuman-1.idx") + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert record.se != null }, + { assert record.scrub_report != null }, + { assert record.special_meta != null }, + { assert snapshot( + record.meta, + record.special_meta, + record.scrub_report, + record.versions + ).match() } + ) + } + } + + test("deacon_filter - module - ERR3772599 - LR") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "ERR3772599"], + r1: null, + r2: null, + se: null, + lr: file("${params.test_data_dir}/species/portiera/reads/nanopore/ERR3772599.fastq.gz") + ) + ) + input[1] = file("${params.test_data_dir}/datasets/deacon/panhuman-1.idx") + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert record.lr != null }, + { assert record.scrub_report != null }, + { assert record.special_meta != null }, + { assert snapshot( + record.meta, + record.special_meta, + record.scrub_report, + record.versions + ).match() } + ) + } + } +} diff --git a/modules/deacon/filter/tests/main.nf.test.snap b/modules/deacon/filter/tests/main.nf.test.snap new file mode 100644 index 000000000..703cfb7b5 --- /dev/null +++ b/modules/deacon/filter/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "deacon_filter - module - ERR3772599 - LR": { + "content": [ + { + "id": "ERR3772599-DEACON_FILTER", + "logs_dir": "ERR3772599/tools/deacon/logs/", + "name": "ERR3772599", + "output_dir": "ERR3772599/tools/deacon", + "process_name": "deacon", + "runtype": "lr", + "scope": "sample", + "single_end": true + }, + { + "name": "ERR3772599" + }, + "ERR3772599.scrub.report.tsv:md5,09560c6e71aa935477497e7c70b09783", + [ + "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" + ] + ], + "timestamp": "2026-05-06T14:35:01.429376554", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "deacon_filter - module - SRR2838702 - SE": { + "content": [ + { + "id": "SRR2838702-DEACON_FILTER", + "logs_dir": "SRR2838702/tools/deacon/logs/", + "name": "SRR2838702", + "output_dir": "SRR2838702/tools/deacon", + "process_name": "deacon", + "runtype": "se", + "scope": "sample", + "single_end": true + }, + { + "name": "SRR2838702" + }, + "SRR2838702.scrub.report.tsv:md5,e410acaf72867214ee63f0e2927141b7", + [ + "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" + ] + ], + "timestamp": "2026-05-06T14:34:44.548001567", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "deacon_filter - module - SRR2838702 - PE": { + "content": [ + { + "id": "SRR2838702-DEACON_FILTER", + "logs_dir": "SRR2838702/tools/deacon/logs/", + "name": "SRR2838702", + "output_dir": "SRR2838702/tools/deacon", + "process_name": "deacon", + "runtype": "paired-end", + "scope": "sample", + "single_end": false + }, + { + "name": "SRR2838702" + }, + "SRR2838702.scrub.report.tsv:md5,fa4967e6660c5d5939e60f387876500f", + [ + "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" + ] + ], + "timestamp": "2026-05-06T14:34:29.120029938", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/deacon/filter/tests/nextflow.config b/modules/deacon/filter/tests/nextflow.config new file mode 100644 index 000000000..642d3e944 --- /dev/null +++ b/modules/deacon/filter/tests/nextflow.config @@ -0,0 +1,36 @@ +// Minimal config for module-level testing of DEACON_FILTER +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "deacon" + logo_name = "bactopia-tools" + description = "Filter host reads from sequencing data" + ext = "fna" + } + + bactopia_version = '4.0.0' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +includeConfig "../module.config" +includeConfig "../../../../conf/base.config" +includeConfig "../../../../conf/profiles.config" diff --git a/modules/deacon/filter/tests/nf-test.config b/modules/deacon/filter/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/modules/deacon/filter/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/modules/deacon/index/main.nf b/modules/deacon/index/main.nf new file mode 100644 index 000000000..e04547b69 --- /dev/null +++ b/modules/deacon/index/main.nf @@ -0,0 +1,69 @@ +/** + * Build a deacon minimizer index from a FASTA reference genome. + * + * Uses [deacon](https://github.com/bede/deacon) to build a minimizer index from a reference + * genome in FASTA format. The resulting index is used by the deacon filter module to remove + * host contamination from sequencing reads via SIMD-accelerated minimizer comparison. + * + * @status stable + * @keywords host, decontamination, depletion, index, minimizer, reference, deacon + * @tags complexity:simple input-type:single output-type:single features:no-test + * @citation deacon + * + * @note Build Once + * This process builds a minimizer index from a reference FASTA. The index is cached + * via storeDir and only needs to be built once per reference genome. + * + * @input reference + * Reference genome in FASTA format to build the minimizer index from + * + * @output record(db, logs) + * - `db`: The built deacon minimizer index file + */ +nextflow.enable.types = true + +// bactopia-lint: ignore M012,M017,M018,M022,M023,M024,M025,M026,M028 +process DEACON_INDEX { + tag "deacon-index" + label 'process_medium' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + reference: Path + + output: + record( + db: file("${prefix}/deacon-index.idx"), + logs: files("${prefix}/logs/*", optional: true) + ) + + script: + prefix = task.ext.process_name + """ + mkdir -p ${prefix}/logs + + deacon \\ + index \\ + build \\ + --threads ${task.cpus} \\ + ${task.ext.args} \\ + ${reference} \\ + > ${prefix}/deacon-index.idx + + # Move outputs to tool specific folder + cp .command.begin ${prefix}/logs/nf.command.begin + cp .command.err ${prefix}/logs/nf.command.err + cp .command.log ${prefix}/logs/nf.command.log + cp .command.out ${prefix}/logs/nf.command.out + cp .command.run ${prefix}/logs/nf.command.run + cp .command.sh ${prefix}/logs/nf.command.sh + cp .command.trace ${prefix}/logs/nf.command.trace + + cat <<-END_VERSIONS > ${prefix}/logs/versions.yml + "${task.process}": + deacon: \$( deacon --version | head -n1 | sed 's/deacon //' ) + END_VERSIONS + """ +} diff --git a/modules/deacon/index/module.config b/modules/deacon/index/module.config new file mode 100644 index 000000000..392dde1e3 --- /dev/null +++ b/modules/deacon/index/module.config @@ -0,0 +1,23 @@ +params { + // deacon_index +} + +process { + withName: 'DEACON_INDEX' { + ext.wf = params.wf + ext.scope = "run" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "deacon_index" + storeDir = params.datasets_cache + + // Tool arguments + ext.args = "" + + // Environment information + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/deacon/index/schema.json b/modules/deacon/index/schema.json new file mode 100644 index 000000000..568b2cf6b --- /dev/null +++ b/modules/deacon/index/schema.json @@ -0,0 +1,29 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/deacon/index/schema.json", + "title": "Deacon Index Module", + "description": "A module for building a deacon minimizer index from a reference genome", + "type": "object", + "$defs": { + "deacon_index_parameters": { + "title": "Deacon Index Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_reference": { + "type": "string", + "default": "", + "description": "Path to a reference genome FASTA file to build the deacon index from", + "fa_icon": "fas fa-font" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/deacon_index_parameters" + } + ] +} diff --git a/modules/kraken2/module.config b/modules/kraken2/module.config index 5d7512d30..8b699b21f 100644 --- a/modules/kraken2/module.config +++ b/modules/kraken2/module.config @@ -35,9 +35,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/nohuman/download/module.config b/modules/nohuman/download/module.config index 8c680c3b5..1050d69d7 100644 --- a/modules/nohuman/download/module.config +++ b/modules/nohuman/download/module.config @@ -2,6 +2,7 @@ params { // nohuman_download download_nohuman = false nohuman_db = null + use_nohuman = false nohuman_db_version = "" nohuman_save_as_tarball = false } @@ -26,9 +27,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/nohuman/run/module.config b/modules/nohuman/run/module.config index 70864337d..8348a4b3f 100644 --- a/modules/nohuman/run/module.config +++ b/modules/nohuman/run/module.config @@ -20,9 +20,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/srahumanscrubber/scrub/module.config b/modules/srahumanscrubber/scrub/module.config index e186baed7..0ecf49139 100644 --- a/modules/srahumanscrubber/scrub/module.config +++ b/modules/srahumanscrubber/scrub/module.config @@ -15,9 +15,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::bactopia-teton=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-teton:1.1.3--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.3--hdfd78af_0" + ext.toolName = "bioconda::bactopia-teton=1.1.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-teton:1.1.4--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-teton:1.1.4--hdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/subworkflows/deacon/main.nf b/subworkflows/deacon/main.nf new file mode 100644 index 000000000..a19efae9b --- /dev/null +++ b/subworkflows/deacon/main.nf @@ -0,0 +1,63 @@ +/** + * Remove host reads from sequencing data using deacon. + * + * This subworkflow uses [deacon](https://github.com/bede/deacon) to identify and remove + * host reads from FASTQ files using SIMD-accelerated minimizer comparison against a + * pre-built reference index (default: panhuman-1). It optionally downloads the index + * if not already available. + * + * @status stable + * @keywords host, contamination, decontamination, depletion, filtering, minimizer, reads, deacon + * @tags complexity:moderate input-type:single output-type:single features:database-dependent,conditional-logic,resource-download + * @citation deacon + * + * @modules deacon_fetch, deacon_filter + * + * @input record(meta, r1?, r2?, se?, lr?) + * - `meta`: Groovy Record containing sample information + * - `r1?`: Illumina R1 reads (paired-end forward) + * - `r2?`: Illumina R2 reads (paired-end reverse) + * - `se?`: Single-end Illumina reads + * - `lr?`: Long reads (ONT/PacBio) + * + * @input database + * Path to deacon minimizer index file (.idx) (ignored if download_deacon is true) + * + * @input download_deacon + * Boolean flag to download the index instead of using the provided path + * + * @output sample_outputs + * - `special_meta`: Simplified metadata record for downstream report joining + * - `r1?`: Filtered paired-end forward reads + * - `r2?`: Filtered paired-end reverse reads + * - `se?`: Filtered single-end reads + * - `lr?`: Filtered long reads + * - `scrub_report`: Read filtering statistics report + * + * @output run_outputs + */ +nextflow.enable.types = true + +include { DEACON_FETCH } from '../../modules/deacon/fetch/main' +include { DEACON_FILTER as DEACON_MODULE } from '../../modules/deacon/filter/main' + +workflow DEACON { + take: + reads: Channel + database: Path? + download_deacon: Boolean + + main: + ch_deacon = channel.empty() + if (download_deacon) { + ch_deacon_fetch = DEACON_FETCH() + ch_deacon = DEACON_MODULE(reads, ch_deacon_fetch.map { r -> r.db }) + } else { + ch_deacon = DEACON_MODULE(reads, database) + } + + emit: + // Published outputs + sample_outputs = ch_deacon + run_outputs = channel.empty() +} diff --git a/subworkflows/deacon/tests/main.nf.test b/subworkflows/deacon/tests/main.nf.test new file mode 100644 index 000000000..8ab57366a --- /dev/null +++ b/subworkflows/deacon/tests/main.nf.test @@ -0,0 +1,44 @@ +nextflow_workflow { + name "Test DEACON Subworkflow" + script "../main.nf" + workflow "DEACON" + tag "subworkflows" + tag "deacon" + + test("deacon - subworkflow - SRR2838702") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "SRR2838702"], + r1: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R1.fastq.gz"), + r2: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R2.fastq.gz"), + se: null, + lr: null + ) + ) + input[1] = file("${params.test_data_dir}/datasets/deacon/panhuman-1.idx") + input[2] = false + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs != null }, + { assert sample.r1 != null }, + { assert sample.r2 != null }, + { assert snapshot( + sample.meta, + sample.versions + ).match() } + ) + } + } +} diff --git a/subworkflows/deacon/tests/main.nf.test.snap b/subworkflows/deacon/tests/main.nf.test.snap new file mode 100644 index 000000000..20a945eaf --- /dev/null +++ b/subworkflows/deacon/tests/main.nf.test.snap @@ -0,0 +1,24 @@ +{ + "deacon - subworkflow - SRR2838702": { + "content": [ + { + "id": "SRR2838702-DEACON:DEACON_MODULE", + "logs_dir": "SRR2838702/tools/deacon/logs/", + "name": "SRR2838702", + "output_dir": "SRR2838702/tools/deacon", + "process_name": "deacon", + "runtype": "paired-end", + "scope": "sample", + "single_end": false + }, + [ + "versions.yml:md5,9d3e1c1b5110e0048698861366ed5151" + ] + ], + "timestamp": "2026-05-06T14:31:09.736499752", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/deacon/tests/nextflow.config b/subworkflows/deacon/tests/nextflow.config new file mode 100644 index 000000000..20af2e44f --- /dev/null +++ b/subworkflows/deacon/tests/nextflow.config @@ -0,0 +1,40 @@ +// Minimal config for subworkflow-level testing of DEACON +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "deacon" + logo_name = "bactopia-tools" + description = "Remove host reads from sequencing data" + ext = "fna" + } + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Load module configs for ALL processes used by this subworkflow +includeConfig "../../../modules/deacon/fetch/module.config" +includeConfig "../../../modules/deacon/filter/module.config" + +// Base config (container resolution + resource labels) +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" + +// Plugin +plugins { + id 'nf-bactopia@2.1.4' +} diff --git a/subworkflows/deacon/tests/nf-test.config b/subworkflows/deacon/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/subworkflows/deacon/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/subworkflows/scrubber/main.nf b/subworkflows/scrubber/main.nf index 6bbf88a15..ece173fe3 100644 --- a/subworkflows/scrubber/main.nf +++ b/subworkflows/scrubber/main.nf @@ -1,18 +1,18 @@ /** * Remove contaminant sequences from metagenomic data. * - * This subworkflow removes human and other contaminant sequences from metagenomic reads using either - * the [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber) or [nohuman](https://github.com/mbhall88/nohuman) - * with the HPRC human database. It provides flexible contamination removal with detailed reporting - * and aggregates results across multiple samples. + * This subworkflow removes human and other contaminant sequences from metagenomic reads using + * [deacon](https://github.com/bede/deacon) (default), [nohuman](https://github.com/mbhall88/nohuman), + * or the [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber). It provides flexible + * contamination removal with detailed reporting and aggregates results across multiple samples. * * @status stable * @keywords metagenomics, decontamination, human removal, read filtering * @tags complexity:moderate input-type:single output-type:multiple features:conditional-logic,aggregation - * @citation kraken2, srahumanscrubber + * @citation deacon, kraken2, srahumanscrubber * * @modules csvtk_concat - * @subworkflows srahumanscrubber, nohuman + * @subworkflows deacon, srahumanscrubber, nohuman * * @input record(meta, r1?, r2?, se?, lr?) * - `meta`: Groovy Record containing sample information @@ -22,10 +22,13 @@ * - `lr?`: Long reads (ONT/PacBio) * * @input use_srascrubber - * Boolean flag to choose between SRA Human Scrubber (true) or nohuman (false) for decontamination. + * Boolean flag to use SRA Human Scrubber for decontamination + * + * @input use_nohuman + * Boolean flag to use nohuman for decontamination * * @input nohuman_db - * Path to nohuman database directory or tarball (used when use_srascrubber is false) + * Path to nohuman database directory or tarball (used when use_nohuman is true) * * @input download_nohuman * Boolean flag to download the nohuman database instead of using the provided path @@ -33,6 +36,12 @@ * @input nohuman_save_as_tarball * Boolean flag to save downloaded nohuman database as tarball * + * @input deacon_db + * Path to deacon minimizer index file (.idx) (used when deacon is selected) + * + * @input download_deacon + * Boolean flag to download the deacon index instead of using the provided path + * * @output sample_outputs * - `special_meta`: Simplified metadata record for downstream report joining * - `r1?`: Scrubbed paired-end forward reads @@ -65,6 +74,7 @@ nextflow.enable.types = true include { SRAHUMANSCRUBBER } from '../srahumanscrubber/main' include { NOHUMAN } from '../nohuman/main' +include { DEACON } from '../deacon/main' include { CSVTK_CONCAT } from '../../modules/csvtk/concat/main' include { gatherCsvtk } from 'plugin/nf-bactopia' include { filterWithData } from 'plugin/nf-bactopia' @@ -73,9 +83,12 @@ workflow SCRUBBER { take: reads: Channel use_srascrubber: Boolean + use_nohuman: Boolean nohuman_db: Path? download_nohuman: Boolean nohuman_save_as_tarball: Boolean + deacon_db: Path? + download_deacon: Boolean main: ch_sample_outputs = channel.empty() @@ -86,10 +99,14 @@ workflow SCRUBBER { ch_srahumanscrubber = SRAHUMANSCRUBBER(ch_reads) ch_sample_outputs = ch_srahumanscrubber.sample_outputs ch_special_report = ch_srahumanscrubber.sample_outputs.map { r -> record(special_meta: r.special_meta, scrub_report: r.scrub_report) } - } else { + } else if (use_nohuman) { ch_nohuman = NOHUMAN(ch_reads, nohuman_db, download_nohuman, nohuman_save_as_tarball) ch_sample_outputs = ch_nohuman.sample_outputs ch_special_report = ch_nohuman.sample_outputs.map { r -> record(special_meta: r.special_meta, scrub_report: r.scrub_report) } + } else { + ch_deacon = DEACON(ch_reads, deacon_db, download_deacon) + ch_sample_outputs = ch_deacon.sample_outputs + ch_special_report = ch_deacon.sample_outputs.map { r -> record(special_meta: r.special_meta, scrub_report: r.scrub_report) } } ch_csvtk_concat = CSVTK_CONCAT(gatherCsvtk(ch_sample_outputs, 'scrub_report', [name: 'scrubber']), 'tsv', 'tsv') diff --git a/subworkflows/scrubber/tests/main.nf.test b/subworkflows/scrubber/tests/main.nf.test index 93b6fc7f2..2db5a3253 100644 --- a/subworkflows/scrubber/tests/main.nf.test +++ b/subworkflows/scrubber/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_workflow { tag "subworkflows" tag "scrubber" - test("scrubber - subworkflow - SRR2838702") { + test("scrubber - subworkflow - SRR2838702 - nohuman") { when { params { test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" @@ -22,9 +22,61 @@ nextflow_workflow { ) ) input[1] = false - input[2] = file("${params.test_data_dir}/datasets/nohuman/HPRC.r2") - input[3] = false + input[2] = true + input[3] = file("${params.test_data_dir}/datasets/nohuman/HPRC.r2") input[4] = false + input[5] = false + input[6] = null + input[7] = false + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def run = workflow.out.run_outputs[0] + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs != null }, + { assert workflow.out.run_outputs != null }, + { assert workflow.out.scrubbed != null }, + { assert workflow.out.special_tsv != null }, + { assert snapshot( + sample.meta, + sample.versions, + run.meta, + run.versions + ).match() }, + { assert sample.scrub_report != null }, + { assert sample.results != null }, + { assert run.results != null } + ) + } + } + + test("scrubber - subworkflow - SRR2838702 - deacon") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "SRR2838702", runtype: "paired-end"], + r1: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R1.fastq.gz"), + r2: file("${params.test_data_dir}/species/portiera/reads/illumina/SRR2838702_R2.fastq.gz"), + se: null, + lr: null + ) + ) + input[1] = false + input[2] = false + input[3] = null + input[4] = false + input[5] = false + input[6] = file("${params.test_data_dir}/datasets/deacon/panhuman-1.idx") + input[7] = false """ } } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index 9625d1afe..91dcc5ae3 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -36,6 +36,8 @@ includeConfig "../../../modules/srahumanscrubber/initdb/module.config" includeConfig "../../../modules/srahumanscrubber/scrub/module.config" includeConfig "../../../modules/nohuman/run/module.config" includeConfig "../../../modules/nohuman/download/module.config" +includeConfig "../../../modules/deacon/fetch/module.config" +includeConfig "../../../modules/deacon/filter/module.config" includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) diff --git a/subworkflows/teton/main.nf b/subworkflows/teton/main.nf index 21192d76b..963be1584 100644 --- a/subworkflows/teton/main.nf +++ b/subworkflows/teton/main.nf @@ -13,7 +13,7 @@ * @status stable * @keywords metagenomics, taxonomy, classification, kraken, bracken, genome size * @tags complexity:complex input-type:single output-type:multiple features:aggregation,database-dependent,conditional-logic - * @citation kraken2, bracken + * @citation deacon, kraken2, bracken * * @modules bactopia_teton, csvtk_join, csvtk_concat * @subworkflows scrubber, bracken @@ -31,6 +31,24 @@ * @input use_srascrubber * Boolean flag to use SRA scrubber for host read removal * + * @input use_nohuman + * Boolean flag to use nohuman for host read removal + * + * @input nohuman_db + * Path to nohuman database directory or tarball + * + * @input download_nohuman + * Boolean flag to download the nohuman database + * + * @input nohuman_save_as_tarball + * Boolean flag to save downloaded nohuman database as tarball + * + * @input deacon_db + * Path to deacon minimizer index file (.idx) + * + * @input download_deacon + * Boolean flag to download the deacon index + * * @output sample_outputs * * @output run_outputs @@ -53,13 +71,16 @@ workflow TETON { reads: Channel db: Path? use_srascrubber: Boolean + use_nohuman: Boolean nohuman_db: Path? download_nohuman: Boolean nohuman_save_as_tarball: Boolean + deacon_db: Path? + download_deacon: Boolean main: // Remove host reads - ch_scrubber = SCRUBBER(reads, use_srascrubber, nohuman_db, download_nohuman, nohuman_save_as_tarball) + ch_scrubber = SCRUBBER(reads, use_srascrubber, use_nohuman, nohuman_db, download_nohuman, nohuman_save_as_tarball, deacon_db, download_deacon) // Taxon Classification & Abundance ch_bracken = BRACKEN(ch_scrubber.scrubbed, db) diff --git a/workflows/bactopia-tools/scrubber/main.nf b/workflows/bactopia-tools/scrubber/main.nf index eb689cfff..011847d7c 100644 --- a/workflows/bactopia-tools/scrubber/main.nf +++ b/workflows/bactopia-tools/scrubber/main.nf @@ -3,16 +3,16 @@ * Removal of human and contaminant sequences from metagenomic reads. * * This Bactopia Tool removes human and other contaminant sequences from metagenomic reads using - * either [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber) or - * [nohuman](https://github.com/mbhall88/nohuman) with the HPRC human database. The tool provides flexible contamination removal - * with detailed reporting of read classification and filtering statistics. It processes paired-end - * or single-end reads, producing cleaned FASTQ files with human sequences removed and comprehensive - * reports documenting the decontamination process. + * [deacon](https://github.com/bede/deacon) (default), [nohuman](https://github.com/mbhall88/nohuman), + * or [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber). The tool provides flexible + * contamination removal with detailed reporting of read classification and filtering statistics. + * It processes paired-end or single-end reads, producing cleaned FASTQ files with human sequences + * removed and comprehensive reports documenting the decontamination process. * * @status stable * @keywords metagenomics, decontamination, human removal, read filtering, bactopia-tool * @tags complexity:moderate input-type:parameter output-type:multiple features:bactopia-tool,aggregation,conditional - * @citation kraken2, srahumanscrubber + * @citation deacon, kraken2, srahumanscrubber * * @subworkflows utils_bactopia-tools, scrubber * @@ -20,7 +20,16 @@ * Directory containing results from a completed Bactopia analysis run * * @input use_srascrubber - * Boolean flag to choose between SRA Human Scrubber (true) or nohuman (false) for decontamination + * Boolean flag to use SRA Human Scrubber for decontamination + * + * @input use_nohuman + * Boolean flag to use nohuman for decontamination + * + * @input deacon_db + * Path to a pre-existing deacon minimizer index (.idx) for host read filtering + * + * @input download_deacon + * Download the deacon index to the datasets cache * * @section Per-Sample Results * @publish *.scrubbed.fastq.gz Cleaned reads after human sequence removal @@ -43,9 +52,12 @@ params { // Tool-specific parameters use_srascrubber : Boolean + use_nohuman : Boolean nohuman_db : Path? download_nohuman : Boolean nohuman_save_as_tarball : Boolean + deacon_db : Path? + download_deacon : Boolean } include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' @@ -58,9 +70,12 @@ workflow { ch_scrubber = SCRUBBER( ch_bactopiatool.reads, params.use_srascrubber, + params.use_nohuman, params.nohuman_db, params.download_nohuman, - params.nohuman_save_as_tarball + params.nohuman_save_as_tarball, + params.deacon_db, + params.download_deacon ) publish: diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index ca107aea5..5983eef1f 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -33,6 +33,8 @@ includeConfig "../../../modules/srahumanscrubber/initdb/module.config" includeConfig "../../../modules/srahumanscrubber/scrub/module.config" includeConfig "../../../modules/nohuman/download/module.config" includeConfig "../../../modules/nohuman/run/module.config" +includeConfig "../../../modules/deacon/fetch/module.config" +includeConfig "../../../modules/deacon/filter/module.config" // Set output directory outputDir = params.outdir @@ -91,4 +93,4 @@ plugins { bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/scrubber/nextflow_schema.json b/workflows/bactopia-tools/scrubber/nextflow_schema.json index 99b311223..0d07bad93 100644 --- a/workflows/bactopia-tools/scrubber/nextflow_schema.json +++ b/workflows/bactopia-tools/scrubber/nextflow_schema.json @@ -139,6 +139,78 @@ } } }, + "deacon_fetch_parameters": { + "title": "Deacon Fetch Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_index_name": { + "type": "string", + "default": "panhuman-1", + "description": "Name of the pre-built deacon index to fetch", + "fa_icon": "fas fa-font" + }, + "download_deacon": { + "type": "boolean", + "default": false, + "description": "Download the deacon index to the datasets cache", + "fa_icon": "fas fa-toggle-on" + }, + "use_deacon": { + "type": "boolean", + "default": false, + "description": "Use deacon for host read filtering", + "fa_icon": "fas fa-toggle-on" + } + } + }, + "deacon_filter_parameters": { + "title": "Deacon Filter Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_abs_threshold": { + "type": "integer", + "default": 2, + "description": "Minimum absolute number of minimizer hits for a match", + "fa_icon": "fas fa-hashtag" + }, + "deacon_db": { + "type": "string", + "default": "", + "description": "Path to a pre-existing deacon index (.idx) for host read filtering", + "fa_icon": "fas fa-font" + }, + "deacon_deplete": { + "type": "boolean", + "default": true, + "description": "Discard matching sequences instead of keeping them", + "fa_icon": "fas fa-toggle-on" + }, + "deacon_opts": { + "type": "string", + "default": "", + "description": "Additional deacon filter options not covered by other parameters", + "fa_icon": "fas fa-font" + }, + "deacon_prefix_length": { + "type": "integer", + "default": 0, + "description": "Search only the first N nucleotides per sequence (0 for all)", + "fa_icon": "fas fa-hashtag" + }, + "deacon_rel_threshold": { + "type": "number", + "default": 0.01, + "description": "Minimum relative proportion (0.0-1.0) of minimizer hits for a match", + "fa_icon": "fas fa-percentage" + } + } + }, "optional_parameters": { "title": "Optional Parameters", "type": "object", @@ -500,6 +572,12 @@ { "$ref": "#/$defs/nohuman_run_parameters" }, + { + "$ref": "#/$defs/deacon_fetch_parameters" + }, + { + "$ref": "#/$defs/deacon_filter_parameters" + }, { "$ref": "#/$defs/optional_parameters" }, @@ -516,4 +594,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/scrubber/tests/.nftignore b/workflows/bactopia-tools/scrubber/tests/.nftignore index 72a5fcb38..dddf0d435 100644 --- a/workflows/bactopia-tools/scrubber/tests/.nftignore +++ b/workflows/bactopia-tools/scrubber/tests/.nftignore @@ -1,3 +1,3 @@ -**/*.{err,gz,html,log,pdf,stderr,stdout} +**/*.{err,gz,html,json,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test b/workflows/bactopia-tools/scrubber/tests/main.nf.test index 4ca9d7f4a..96e571650 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test @@ -6,11 +6,47 @@ nextflow_pipeline { tag "bactopia-tools" tag "scrubber" + test("Scrubber (deacon) - SRR2838702|portiera|compressed_fastq") { + when { + params { + bactopia_test = "/species/portiera/compressed" + deacon_test = "/datasets/deacon/panhuman-1.idx" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + test("Scrubber (nohuman) - SRR2838702|portiera|compressed_fastq") { when { params { bactopia_test = "/species/portiera/compressed" - nohuman_test = "/datasets/nohuman/HPRC.r2" + nohuman_test = "/datasets/nohuman/HPRC.r2/db" test_dataset = "" test_dataset2 = "" test_dataset3 = "" @@ -20,6 +56,7 @@ nextflow_pipeline { test_ont = "" is_ci = true outdir = "$outputDir" + use_nohuman = true } } diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap index f747af7a5..95304432e 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap @@ -1,4 +1,56 @@ { + "Scrubber (deacon) - SRR2838702|portiera|compressed_fastq": { + "content": [ + 2, + [ + "SRR2838702", + "SRR2838702/tools", + "SRR2838702/tools/scrubber", + "SRR2838702/tools/scrubber/SRR2838702.deacon.json", + "SRR2838702/tools/scrubber/SRR2838702.scrub.report.tsv", + "SRR2838702/tools/scrubber/SRR2838702_R1.scrubbed.fastq.gz", + "SRR2838702/tools/scrubber/SRR2838702_R2.scrubbed.fastq.gz", + "SRR2838702/tools/scrubber/logs", + "SRR2838702/tools/scrubber/logs/nf.command.begin", + "SRR2838702/tools/scrubber/logs/nf.command.err", + "SRR2838702/tools/scrubber/logs/nf.command.log", + "SRR2838702/tools/scrubber/logs/nf.command.out", + "SRR2838702/tools/scrubber/logs/nf.command.run", + "SRR2838702/tools/scrubber/logs/nf.command.sh", + "SRR2838702/tools/scrubber/logs/nf.command.trace", + "SRR2838702/tools/scrubber/logs/versions.yml", + "bactopia-runs", + "bactopia-runs/scrubber", + "bactopia-runs/scrubber/merged-results", + "bactopia-runs/scrubber/merged-results/logs", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.begin", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.err", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.log", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.out", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.run", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.sh", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/nf.command.trace", + "bactopia-runs/scrubber/merged-results/logs/scrubber-concat/versions.yml", + "bactopia-runs/scrubber/merged-results/scrubber.tsv", + "bactopia-runs/scrubber/nf-reports", + "bactopia-runs/scrubber/nf-reports/scrubber-dag.dot", + "bactopia-runs/scrubber/nf-reports/scrubber-report.html", + "bactopia-runs/scrubber/nf-reports/scrubber-timeline.html" + ], + [ + "SRR2838702.scrub.report.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d", + "versions.yml:md5,e07f44b8fe13644174f75b5cc7193f10", + "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5", + "scrubber.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d" + ] + ], + "timestamp": "2026-05-06T15:45:32.588701069", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, "Scrubber (nohuman) - SRR2838702|portiera|compressed_fastq": { "content": [ 2, @@ -39,12 +91,12 @@ ], [ "SRR2838702.scrub.report.tsv:md5,e957775ff85716621f5fdd536de5b417", - "versions.yml:md5,a8320e62273b53dca9cfffcb088d3ebb", + "versions.yml:md5,02561307297f583bd0d158052302fcf0", "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5", "scrubber.tsv:md5,e957775ff85716621f5fdd536de5b417" ] ], - "timestamp": "2026-04-29T11:26:47.921737698", + "timestamp": "2026-05-06T15:48:31.038388568", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +147,7 @@ "scrubber.tsv:md5,9554a4a6929bbfd485e28acd4a716772" ] ], - "timestamp": "2026-04-29T11:27:14.371261957", + "timestamp": "2026-05-06T15:49:11.183710425", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/cleanyerreads/main.nf b/workflows/cleanyerreads/main.nf index 145a7c308..a5a7e58e6 100644 --- a/workflows/cleanyerreads/main.nf +++ b/workflows/cleanyerreads/main.nf @@ -4,14 +4,15 @@ * * This workflow performs comprehensive read quality control including trimming, * adapter removal, quality filtering, and optionally removes host contamination - * using [nohuman](https://github.com/mbhall88/nohuman) or [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber). + * using [deacon](https://github.com/bede/deacon), [nohuman](https://github.com/mbhall88/nohuman), + * or [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber). * It processes raw sequencing reads to produce high-quality clean reads ready * for downstream analysis. * * @status stable * @keywords reads, quality control, trimming, filtering, host removal, preprocessing * @tags complexity:moderate input-type:parameter output-type:multiple features:aggregation,conditional-logic,database-dependent - * @citation bbtools, fastp, fastqc, fastq_scan, kraken2, lighter, nanoplot, nanoq, porechop, rasusa, srahumanscrubber + * @citation bbtools, deacon, fastp, fastqc, fastq_scan, kraken2, lighter, nanoplot, nanoq, porechop, rasusa, srahumanscrubber * * @subworkflows utils_bactopia, bactopia_gather, bactopia_qc, scrubber * @@ -24,6 +25,9 @@ * @input use_srascrubber * Remove host reads using SRA Human Scrubber * + * @input use_deacon + * Remove host reads using deacon with minimizer-based filtering + * * @input nohuman_db * Path to a pre-built nohuman HPRC database * @@ -33,6 +37,12 @@ * @input nohuman_save_as_tarball * Save the downloaded nohuman database as a tarball for reuse * + * @input deacon_db + * Path to a pre-existing deacon minimizer index (.idx) for host read filtering + * + * @input download_deacon + * Download the deacon index to the datasets cache + * * @input adapters * Path to adapter sequences file for removal * @@ -70,11 +80,14 @@ params { // Tool-specific parameters use_nohuman : Boolean use_srascrubber : Boolean + use_deacon : Boolean adapters : Path? phix : Path? nohuman_db : Path? download_nohuman : Boolean nohuman_save_as_tarball : Boolean + deacon_db : Path? + download_deacon : Boolean } // Core @@ -97,14 +110,17 @@ workflow { ch_sample_outputs = ch_gather.sample_outputs ch_run_outputs = ch_gather.run_outputs - if (params.use_nohuman || params.use_srascrubber) { + if (params.use_nohuman || params.use_srascrubber || params.use_deacon) { // Remove host reads ch_scrubber = SCRUBBER( ch_gather.reads, params.use_srascrubber, + params.use_nohuman, params.nohuman_db, params.download_nohuman, - params.nohuman_save_as_tarball + params.nohuman_save_as_tarball, + params.deacon_db, + params.download_deacon ) ch_sample_outputs = ch_sample_outputs.mix(ch_scrubber.sample_outputs) ch_run_outputs = ch_run_outputs.mix(ch_scrubber.run_outputs) diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index e05f06dd5..de251a32c 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -34,6 +34,8 @@ includeConfig "../../modules/srahumanscrubber/initdb/module.config" includeConfig "../../modules/srahumanscrubber/scrub/module.config" includeConfig "../../modules/nohuman/download/module.config" includeConfig "../../modules/nohuman/run/module.config" +includeConfig "../../modules/deacon/fetch/module.config" +includeConfig "../../modules/deacon/filter/module.config" // Workflow specific params.config includeConfig "../../conf/params/cleanyerreads.config" @@ -95,4 +97,4 @@ plugins { bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/cleanyerreads/nextflow_schema.json b/workflows/cleanyerreads/nextflow_schema.json index f1d15e1f4..374919178 100644 --- a/workflows/cleanyerreads/nextflow_schema.json +++ b/workflows/cleanyerreads/nextflow_schema.json @@ -514,6 +514,87 @@ } } }, + "deacon_fetch_parameters": { + "title": "Deacon Fetch Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_index_name": { + "type": "string", + "default": "panhuman-1", + "description": "Name of the pre-built deacon index to fetch", + "fa_icon": "fas fa-font", + "hidden": true + }, + "download_deacon": { + "type": "boolean", + "default": false, + "description": "Download the deacon index to the datasets cache", + "fa_icon": "fas fa-toggle-on", + "hidden": true + }, + "use_deacon": { + "type": "boolean", + "default": false, + "description": "Use deacon for host read filtering", + "fa_icon": "fas fa-toggle-on", + "hidden": true + } + } + }, + "deacon_filter_parameters": { + "title": "Deacon Filter Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_abs_threshold": { + "type": "integer", + "default": 2, + "description": "Minimum absolute number of minimizer hits for a match", + "fa_icon": "fas fa-hashtag", + "hidden": true + }, + "deacon_db": { + "type": "string", + "default": "", + "description": "Path to a pre-existing deacon index (.idx) for host read filtering", + "fa_icon": "fas fa-font", + "hidden": true + }, + "deacon_deplete": { + "type": "boolean", + "default": true, + "description": "Discard matching sequences instead of keeping them", + "fa_icon": "fas fa-toggle-on", + "hidden": true + }, + "deacon_opts": { + "type": "string", + "default": "", + "description": "Additional deacon filter options not covered by other parameters", + "fa_icon": "fas fa-font", + "hidden": true + }, + "deacon_prefix_length": { + "type": "integer", + "default": 0, + "description": "Search only the first N nucleotides per sequence (0 for all)", + "fa_icon": "fas fa-hashtag", + "hidden": true + }, + "deacon_rel_threshold": { + "type": "number", + "default": 0.01, + "description": "Minimum relative proportion (0.0-1.0) of minimizer hits for a match", + "fa_icon": "fas fa-percentage", + "hidden": true + } + } + }, "optional_parameters": { "title": "Optional Parameters", "type": "object", @@ -878,6 +959,12 @@ { "$ref": "#/$defs/nohuman_run_parameters" }, + { + "$ref": "#/$defs/deacon_fetch_parameters" + }, + { + "$ref": "#/$defs/deacon_filter_parameters" + }, { "$ref": "#/$defs/optional_parameters" }, diff --git a/workflows/cleanyerreads/tests/main.nf.test.snap b/workflows/cleanyerreads/tests/main.nf.test.snap index 2d681f72a..2ea5ec100 100644 --- a/workflows/cleanyerreads/tests/main.nf.test.snap +++ b/workflows/cleanyerreads/tests/main.nf.test.snap @@ -87,7 +87,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-04-29T11:27:05.694544", + "timestamp": "2026-05-06T14:41:16.282494509", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -163,7 +163,7 @@ "versions.yml:md5,61924107a406c136f55c445d470721f7" ] ], - "timestamp": "2026-04-29T11:26:09.174329984", + "timestamp": "2026-05-06T14:40:34.994298384", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/teton/main.nf b/workflows/teton/main.nf index d8ba404cb..95d992869 100644 --- a/workflows/teton/main.nf +++ b/workflows/teton/main.nf @@ -4,13 +4,14 @@ * * This workflow performs metagenomic classification using [Kraken2](https://github.com/DerrickWood/kraken2) * and [Bracken](https://github.com/jenniferlu717/Bracken), with optional host read removal - * using SRA Scrubber. It processes metagenomic sequencing reads to estimate bacterial - * genome sizes and separate bacterial from non-bacterial organisms. + * using [deacon](https://github.com/bede/deacon) (default), [nohuman](https://github.com/mbhall88/nohuman), + * or [SRA Human Scrubber](https://github.com/ncbi/sra-human-scrubber). It processes metagenomic + * sequencing reads to estimate bacterial genome sizes and separate bacterial from non-bacterial organisms. * * @status stable * @keywords metagenomics, classification, kraken2, bracken, abundance, profiling * @tags complexity:complex input-type:parameter output-type:multiple features:aggregation,conditional-logic,database-dependent - * @citation bracken, kraken2, srahumanscrubber + * @citation bracken, deacon, kraken2, srahumanscrubber * * @subworkflows utils_bactopia, bactopia_gather, teton * @@ -21,7 +22,10 @@ * Path to Kraken2 database for classification * * @input use_srascrubber - * Remove host reads using SRA scrubber before classification + * Use SRA Human Scrubber for host read removal + * + * @input use_nohuman + * Use nohuman for host read removal * * @input nohuman_db * Path to a pre-built nohuman HPRC database for host read removal @@ -32,6 +36,12 @@ * @input nohuman_save_as_tarball * Save the downloaded nohuman database as a tarball for reuse * + * @input deacon_db + * Path to a pre-existing deacon minimizer index (.idx) for host read filtering + * + * @input download_deacon + * Download the deacon index to the datasets cache + * * @section Per-Sample Results * @publish bacteria.tsv Per-sample TSV files containing bacterial organisms and their properties * @publish nonbacteria.tsv Per-sample TSV files containing non-bacterial organisms @@ -58,9 +68,12 @@ params { // Tool-specific parameters kraken2_db : Path use_srascrubber : Boolean + use_nohuman : Boolean nohuman_db : Path? download_nohuman : Boolean nohuman_save_as_tarball : Boolean + deacon_db : Path? + download_deacon : Boolean } include { BACTOPIA_INIT } from '../../subworkflows/utils/bactopia' @@ -80,9 +93,12 @@ workflow { ch_gather.reads, params.kraken2_db, params.use_srascrubber, + params.use_nohuman, params.nohuman_db, params.download_nohuman, - params.nohuman_save_as_tarball + params.nohuman_save_as_tarball, + params.deacon_db, + params.download_deacon ) // Collect all outputs diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 484012780..6d1ad9e5e 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -35,6 +35,8 @@ includeConfig "../../modules/srahumanscrubber/initdb/module.config" includeConfig "../../modules/srahumanscrubber/scrub/module.config" includeConfig "../../modules/nohuman/download/module.config" includeConfig "../../modules/nohuman/run/module.config" +includeConfig "../../modules/deacon/fetch/module.config" +includeConfig "../../modules/deacon/filter/module.config" includeConfig "../../modules/bracken/module.config" // Workflow specific params.config @@ -97,4 +99,4 @@ plugins { bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} +} \ No newline at end of file diff --git a/workflows/teton/nextflow_schema.json b/workflows/teton/nextflow_schema.json index 43aaef680..d453f7fa2 100644 --- a/workflows/teton/nextflow_schema.json +++ b/workflows/teton/nextflow_schema.json @@ -269,6 +269,87 @@ } } }, + "deacon_fetch_parameters": { + "title": "Deacon Fetch Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_index_name": { + "type": "string", + "default": "panhuman-1", + "description": "Name of the pre-built deacon index to fetch", + "fa_icon": "fas fa-font", + "hidden": true + }, + "download_deacon": { + "type": "boolean", + "default": false, + "description": "Download the deacon index to the datasets cache", + "fa_icon": "fas fa-toggle-on", + "hidden": true + }, + "use_deacon": { + "type": "boolean", + "default": false, + "description": "Use deacon for host read filtering", + "fa_icon": "fas fa-toggle-on", + "hidden": true + } + } + }, + "deacon_filter_parameters": { + "title": "Deacon Filter Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "deacon_abs_threshold": { + "type": "integer", + "default": 2, + "description": "Minimum absolute number of minimizer hits for a match", + "fa_icon": "fas fa-hashtag", + "hidden": true + }, + "deacon_db": { + "type": "string", + "default": "", + "description": "Path to a pre-existing deacon index (.idx) for host read filtering", + "fa_icon": "fas fa-font", + "hidden": true + }, + "deacon_deplete": { + "type": "boolean", + "default": true, + "description": "Discard matching sequences instead of keeping them", + "fa_icon": "fas fa-toggle-on", + "hidden": true + }, + "deacon_opts": { + "type": "string", + "default": "", + "description": "Additional deacon filter options not covered by other parameters", + "fa_icon": "fas fa-font", + "hidden": true + }, + "deacon_prefix_length": { + "type": "integer", + "default": 0, + "description": "Search only the first N nucleotides per sequence (0 for all)", + "fa_icon": "fas fa-hashtag", + "hidden": true + }, + "deacon_rel_threshold": { + "type": "number", + "default": 0.01, + "description": "Minimum relative proportion (0.0-1.0) of minimizer hits for a match", + "fa_icon": "fas fa-percentage", + "hidden": true + } + } + }, "kraken2_bracken_parameters": { "title": "Kraken2 and Bracken Parameters", "type": "object", @@ -761,6 +842,12 @@ { "$ref": "#/$defs/nohuman_run_parameters" }, + { + "$ref": "#/$defs/deacon_fetch_parameters" + }, + { + "$ref": "#/$defs/deacon_filter_parameters" + }, { "$ref": "#/$defs/kraken2_bracken_parameters" }, diff --git a/workflows/teton/tests/main.nf.test b/workflows/teton/tests/main.nf.test index 982c847ea..e425b09bb 100644 --- a/workflows/teton/tests/main.nf.test +++ b/workflows/teton/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { params { bactopia_test = "" test_dataset = "/datasets/kraken2/k2_standard_08_GB_20251015" - nohuman_test = "/datasets/nohuman/HPRC.r2" + deacon_test = "/datasets/deacon/panhuman-1.idx" test_dataset2 = "" test_dataset3 = "" test_r1 = "/species/portiera/compressed/SRR2838702/main/qc/SRR2838702_R1.fastq.gz" @@ -44,6 +44,46 @@ nextflow_pipeline { } } + test("teton (pe+nohuman) - SRR2838702|portiera|compressed_fastq") { + when { + params { + bactopia_test = "" + test_dataset = "/datasets/kraken2/k2_standard_08_GB_20251015" + nohuman_test = "/datasets/nohuman/HPRC.r2/db" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "/species/portiera/compressed/SRR2838702/main/qc/SRR2838702_R1.fastq.gz" + test_r2 = "/species/portiera/compressed/SRR2838702/main/qc/SRR2838702_R2.fastq.gz" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + sample = "SRR2838702" + genome_size = 358242 + min_coverage = 10 + use_nohuman = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + test("teton (pe+srascrubber) - SRR2838702|portiera|compressed_fastq") { when { params { diff --git a/workflows/teton/tests/main.nf.test.snap b/workflows/teton/tests/main.nf.test.snap index cb6a3b427..383e97382 100644 --- a/workflows/teton/tests/main.nf.test.snap +++ b/workflows/teton/tests/main.nf.test.snap @@ -50,19 +50,20 @@ "SRR2838702/teton/tools/bracken/logs/nf.command.trace", "SRR2838702/teton/tools/bracken/logs/versions.yml", "SRR2838702/tools", - "SRR2838702/tools/nohuman", - "SRR2838702/tools/nohuman/SRR2838702.scrub.report.tsv", - "SRR2838702/tools/nohuman/SRR2838702_R1.scrubbed.fastq.gz", - "SRR2838702/tools/nohuman/SRR2838702_R2.scrubbed.fastq.gz", - "SRR2838702/tools/nohuman/logs", - "SRR2838702/tools/nohuman/logs/nf.command.begin", - "SRR2838702/tools/nohuman/logs/nf.command.err", - "SRR2838702/tools/nohuman/logs/nf.command.log", - "SRR2838702/tools/nohuman/logs/nf.command.out", - "SRR2838702/tools/nohuman/logs/nf.command.run", - "SRR2838702/tools/nohuman/logs/nf.command.sh", - "SRR2838702/tools/nohuman/logs/nf.command.trace", - "SRR2838702/tools/nohuman/logs/versions.yml", + "SRR2838702/tools/scrubber", + "SRR2838702/tools/scrubber/SRR2838702.deacon.json", + "SRR2838702/tools/scrubber/SRR2838702.scrub.report.tsv", + "SRR2838702/tools/scrubber/SRR2838702_R1.scrubbed.fastq.gz", + "SRR2838702/tools/scrubber/SRR2838702_R2.scrubbed.fastq.gz", + "SRR2838702/tools/scrubber/logs", + "SRR2838702/tools/scrubber/logs/nf.command.begin", + "SRR2838702/tools/scrubber/logs/nf.command.err", + "SRR2838702/tools/scrubber/logs/nf.command.log", + "SRR2838702/tools/scrubber/logs/nf.command.out", + "SRR2838702/tools/scrubber/logs/nf.command.run", + "SRR2838702/tools/scrubber/logs/nf.command.sh", + "SRR2838702/tools/scrubber/logs/nf.command.trace", + "SRR2838702/tools/scrubber/logs/versions.yml", "bactopia-runs", "bactopia-runs/teton", "bactopia-runs/teton/merged-results", @@ -167,8 +168,8 @@ [ "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", - "versions.yml:md5,8dc4d8979e0dba7fc7b975f9953a3161", - "versions.yml:md5,0e919355c3b46201c37e019227934b1b", + "versions.yml:md5,7d27773f1e349726172140b0c615a73b", + "versions.yml:md5,b567c9f0928098cfc68f12308a3372f0", "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", "versions.yml:md5,61924107a406c136f55c445d470721f7", @@ -180,7 +181,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-04-29T11:31:16.523191261", + "timestamp": "2026-05-06T15:20:19.345378436", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -354,7 +355,7 @@ [ "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", - "versions.yml:md5,8dc4d8979e0dba7fc7b975f9953a3161", + "versions.yml:md5,7d27773f1e349726172140b0c615a73b", "versions.yml:md5,5ccb1a29e9b0dfff5b4a46a6e73facf3", "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", @@ -367,7 +368,194 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-04-29T11:36:04.108243862", + "timestamp": "2026-05-06T15:30:11.50655874", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "teton (pe+nohuman) - SRR2838702|portiera|compressed_fastq": { + "content": [ + 13, + [ + "SRR2838702", + "SRR2838702/teton", + "SRR2838702/teton/main", + "SRR2838702/teton/main/gather", + "SRR2838702/teton/main/gather/SRR2838702-meta.tsv", + 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"merged-results/logs/SRR2838702-join/nf.command.err", + "merged-results/logs/SRR2838702-join/nf.command.log", + "merged-results/logs/SRR2838702-join/nf.command.out", + "merged-results/logs/SRR2838702-join/nf.command.run", + "merged-results/logs/SRR2838702-join/nf.command.sh", + "merged-results/logs/SRR2838702-join/nf.command.trace", + "merged-results/logs/SRR2838702-join/versions.yml" + ], + [ + "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", + "versions.yml:md5,7d27773f1e349726172140b0c615a73b", + "versions.yml:md5,14feb3b47ba66dc6b247bdd7debcc18c", + "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", + "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", + "versions.yml:md5,61924107a406c136f55c445d470721f7", + "versions.yml:md5,b529c3993efa987da9a980fe7c8061f8", + "versions.yml:md5,7365b17a2c11eb3d256b0facd20a197a", + "versions.yml:md5,340e424aa721674cf14433027027114a", + "versions.yml:md5,f27b3200ffeb3e669ad225b87cedf06c", + "versions.yml:md5,fcfb282f67fc93a18b7d921d22e70628", + "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" + ] + ], + "timestamp": "2026-05-06T15:26:01.705868003", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From f06ea0b4d55367ea670701e875e2683ca306ce3b Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 6 May 2026 15:55:36 -0600 Subject: [PATCH 11/43] bump plugin version --- catalog.json | 2 +- nextflow.config | 2 +- subworkflows/abricate/tests/nextflow.config | 2 +- subworkflows/abritamr/tests/nextflow.config | 2 +- subworkflows/agrvate/tests/nextflow.config | 2 +- subworkflows/amrfinderplus/tests/nextflow.config | 2 +- subworkflows/ariba/tests/nextflow.config | 2 +- subworkflows/bactopia/assembler/tests/nextflow.config | 2 +- subworkflows/bactopia/qc/tests/nextflow.config | 2 +- subworkflows/bactopia/sketcher/tests/nextflow.config | 2 +- subworkflows/bakta/tests/nextflow.config | 2 +- subworkflows/blastn/tests/nextflow.config | 2 +- subworkflows/blastp/tests/nextflow.config | 2 +- subworkflows/blastx/tests/nextflow.config | 2 +- subworkflows/bracken/tests/nextflow.config | 2 +- subworkflows/btyper3/tests/nextflow.config | 2 +- subworkflows/busco/tests/nextflow.config | 2 +- subworkflows/checkm/tests/nextflow.config | 2 +- subworkflows/checkm2/tests/nextflow.config | 2 +- subworkflows/clermontyping/tests/nextflow.config | 2 +- subworkflows/clonalframeml/tests/nextflow.config | 2 +- subworkflows/deacon/tests/nextflow.config | 2 +- subworkflows/defensefinder/tests/nextflow.config | 2 +- subworkflows/ectyper/tests/nextflow.config | 2 +- subworkflows/eggnog/tests/nextflow.config | 2 +- subworkflows/emmtyper/tests/nextflow.config | 2 +- subworkflows/fastani/tests/nextflow.config | 2 +- subworkflows/gamma/tests/nextflow.config | 2 +- subworkflows/genotyphi/tests/nextflow.config | 2 +- subworkflows/gigatyper/tests/nextflow.config | 2 +- subworkflows/gtdb/tests/nextflow.config | 2 +- subworkflows/gubbins/tests/nextflow.config | 2 +- subworkflows/hicap/tests/nextflow.config | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 2 +- subworkflows/iqtree/tests/nextflow.config | 2 +- subworkflows/ismapper/tests/nextflow.config | 2 +- subworkflows/kleborate/tests/nextflow.config | 2 +- subworkflows/kraken2/tests/nextflow.config | 2 +- subworkflows/legsta/tests/nextflow.config | 2 +- subworkflows/lissero/tests/nextflow.config | 2 +- subworkflows/mashdist/tests/nextflow.config | 2 +- subworkflows/mashtree/tests/nextflow.config | 2 +- subworkflows/mcroni/tests/nextflow.config | 2 +- subworkflows/meningotype/tests/nextflow.config | 2 +- subworkflows/merlin/tests/nextflow.config | 2 +- subworkflows/merlindist/tests/nextflow.config | 2 +- subworkflows/midas/tests/nextflow.config | 2 +- subworkflows/mlst/tests/nextflow.config | 2 +- subworkflows/mobsuite/tests/nextflow.config | 2 +- subworkflows/mykrobe/tests/nextflow.config | 2 +- subworkflows/ncbigenomedownload/tests/nextflow.config | 2 +- subworkflows/ngmaster/tests/nextflow.config | 2 +- subworkflows/nohuman/tests/nextflow.config | 2 +- subworkflows/panaroo/tests/nextflow.config | 2 +- subworkflows/pangenome/tests/nextflow.config | 2 +- subworkflows/pasty/tests/nextflow.config | 2 +- subworkflows/pbptyper/tests/nextflow.config | 2 +- subworkflows/phispy/tests/nextflow.config | 2 +- subworkflows/pirate/tests/nextflow.config | 2 +- subworkflows/plasmidfinder/tests/nextflow.config | 2 +- subworkflows/pneumocat/tests/nextflow.config | 2 +- subworkflows/prokka/tests/nextflow.config | 2 +- subworkflows/quast/tests/nextflow.config | 2 +- subworkflows/rgi/tests/nextflow.config | 2 +- subworkflows/roary/tests/nextflow.config | 2 +- subworkflows/sccmec/tests/nextflow.config | 2 +- subworkflows/scoary/tests/nextflow.config | 2 +- subworkflows/scrubber/tests/nextflow.config | 2 +- subworkflows/seqsero2/tests/nextflow.config | 2 +- subworkflows/seroba/tests/nextflow.config | 2 +- subworkflows/shigapass/tests/nextflow.config | 2 +- subworkflows/shigatyper/tests/nextflow.config | 2 +- subworkflows/shigeifinder/tests/nextflow.config | 2 +- subworkflows/sistr/tests/nextflow.config | 2 +- subworkflows/snippy/core/tests/nextflow.config | 2 +- subworkflows/snippy/run/tests/nextflow.config | 2 +- subworkflows/snpdists/tests/nextflow.config | 2 +- subworkflows/spatyper/tests/nextflow.config | 2 +- subworkflows/srahumanscrubber/tests/nextflow.config | 2 +- subworkflows/ssuissero/tests/nextflow.config | 2 +- subworkflows/staphopiasccmec/tests/nextflow.config | 2 +- subworkflows/staphscan/tests/nextflow.config | 2 +- subworkflows/staphtyper/tests/nextflow.config | 2 +- subworkflows/stecfinder/tests/nextflow.config | 2 +- subworkflows/sylph/tests/nextflow.config | 2 +- subworkflows/tblastn/tests/nextflow.config | 2 +- subworkflows/tblastx/tests/nextflow.config | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 2 +- subworkflows/teton/tests/nextflow.config | 2 +- subworkflows/traitar/tests/nextflow.config | 2 +- workflows/bactopia-tools/abricate/nextflow.config | 2 +- workflows/bactopia-tools/abritamr/nextflow.config | 2 +- workflows/bactopia-tools/agrvate/nextflow.config | 2 +- workflows/bactopia-tools/amrfinderplus/nextflow.config | 2 +- workflows/bactopia-tools/ariba/nextflow.config | 2 +- workflows/bactopia-tools/bakta/nextflow.config | 2 +- workflows/bactopia-tools/blastn/nextflow.config | 2 +- workflows/bactopia-tools/blastp/nextflow.config | 2 +- workflows/bactopia-tools/blastx/nextflow.config | 2 +- workflows/bactopia-tools/bracken/nextflow.config | 2 +- workflows/bactopia-tools/btyper3/nextflow.config | 2 +- workflows/bactopia-tools/busco/nextflow.config | 2 +- workflows/bactopia-tools/checkm/nextflow.config | 2 +- workflows/bactopia-tools/checkm2/nextflow.config | 2 +- workflows/bactopia-tools/clermontyping/nextflow.config | 2 +- workflows/bactopia-tools/defensefinder/nextflow.config | 2 +- workflows/bactopia-tools/ectyper/nextflow.config | 2 +- workflows/bactopia-tools/eggnog/nextflow.config | 2 +- workflows/bactopia-tools/emmtyper/nextflow.config | 2 +- workflows/bactopia-tools/fastani/nextflow.config | 2 +- workflows/bactopia-tools/gamma/nextflow.config | 2 +- workflows/bactopia-tools/genotyphi/nextflow.config | 2 +- workflows/bactopia-tools/gigatyper/nextflow.config | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 2 +- workflows/bactopia-tools/hicap/nextflow.config | 2 +- workflows/bactopia-tools/hpsuissero/nextflow.config | 2 +- workflows/bactopia-tools/ismapper/nextflow.config | 2 +- workflows/bactopia-tools/kleborate/nextflow.config | 2 +- workflows/bactopia-tools/kraken2/nextflow.config | 2 +- workflows/bactopia-tools/legsta/nextflow.config | 2 +- workflows/bactopia-tools/lissero/nextflow.config | 2 +- workflows/bactopia-tools/mashdist/nextflow.config | 2 +- workflows/bactopia-tools/mashtree/nextflow.config | 2 +- workflows/bactopia-tools/mcroni/nextflow.config | 2 +- workflows/bactopia-tools/meningotype/nextflow.config | 2 +- workflows/bactopia-tools/merlin/nextflow.config | 2 +- workflows/bactopia-tools/midas/nextflow.config | 2 +- workflows/bactopia-tools/mlst/nextflow.config | 2 +- workflows/bactopia-tools/mobsuite/nextflow.config | 2 +- workflows/bactopia-tools/mykrobe/nextflow.config | 2 +- workflows/bactopia-tools/ngmaster/nextflow.config | 2 +- workflows/bactopia-tools/pangenome/nextflow.config | 2 +- workflows/bactopia-tools/pasty/nextflow.config | 2 +- workflows/bactopia-tools/pbptyper/nextflow.config | 2 +- workflows/bactopia-tools/phispy/nextflow.config | 2 +- workflows/bactopia-tools/plasmidfinder/nextflow.config | 2 +- workflows/bactopia-tools/pneumocat/nextflow.config | 2 +- workflows/bactopia-tools/prokka/nextflow.config | 2 +- workflows/bactopia-tools/quast/nextflow.config | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 2 +- workflows/bactopia-tools/sccmec/nextflow.config | 2 +- workflows/bactopia-tools/scrubber/nextflow.config | 4 ++-- workflows/bactopia-tools/seqsero2/nextflow.config | 2 +- workflows/bactopia-tools/seroba/nextflow.config | 2 +- workflows/bactopia-tools/shigapass/nextflow.config | 2 +- workflows/bactopia-tools/shigatyper/nextflow.config | 2 +- workflows/bactopia-tools/shigeifinder/nextflow.config | 2 +- workflows/bactopia-tools/sistr/nextflow.config | 2 +- workflows/bactopia-tools/snippy/nextflow.config | 2 +- workflows/bactopia-tools/spatyper/nextflow.config | 2 +- workflows/bactopia-tools/ssuissero/nextflow.config | 2 +- workflows/bactopia-tools/staphscan/nextflow.config | 2 +- workflows/bactopia-tools/staphtyper/nextflow.config | 2 +- workflows/bactopia-tools/stecfinder/nextflow.config | 2 +- workflows/bactopia-tools/sylph/nextflow.config | 2 +- workflows/bactopia-tools/tblastn/nextflow.config | 2 +- workflows/bactopia-tools/tblastx/nextflow.config | 2 +- workflows/bactopia-tools/tbprofiler/nextflow.config | 2 +- workflows/bactopia-tools/traitar/nextflow.config | 2 +- workflows/cleanyerreads/nextflow.config | 4 ++-- workflows/staphopia/nextflow.config | 2 +- workflows/teton/nextflow.config | 4 ++-- 162 files changed, 165 insertions(+), 165 deletions(-) diff --git a/catalog.json b/catalog.json index 5a0cb754d..8915088d2 100644 --- a/catalog.json +++ b/catalog.json @@ -3,7 +3,7 @@ "generated": "2026-05-06T20:36:40Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.1.6", - "nf_bactopia_version": "2.1.4", + "nf_bactopia_version": "2.1.5", "modules": { "abricate_run": { "description": "Mass screening of contigs for antimicrobial and virulence genes.", diff --git a/nextflow.config b/nextflow.config index 264ab2d82..c960c3541 100644 --- a/nextflow.config +++ b/nextflow.config @@ -118,7 +118,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index 91139faf3..62e8b1ea3 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index bd7f3d574..025ce8d51 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index 4e733b30d..5bfc14a35 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index 2d14a5184..f15694d24 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index 4b5aa17e6..753ec333b 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index 80f53e66a..93bd49596 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -67,5 +67,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index 092b04ab6..3855a1308 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -73,5 +73,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index be2bd89cf..15cda5354 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index ba467c5b3..f21f9249c 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index 8dd8ae098..14ddb6c9d 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index 6ef85fdb7..05f1580b2 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index cc4973238..e88bbb9bd 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index 655db915e..c75a26018 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index 505496a52..01c023876 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index 8a403df12..ef6601e60 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index 347c49d55..27ad7278c 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index a2a3e6b17..aa1884f34 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index feeaaf8da..4db815d33 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index 8dc11b2e7..0f096fd57 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/deacon/tests/nextflow.config b/subworkflows/deacon/tests/nextflow.config index 20af2e44f..76bafcd79 100644 --- a/subworkflows/deacon/tests/nextflow.config +++ b/subworkflows/deacon/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index 293573f8f..7d6adc872 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index 4e4c7111f..8350a5e2a 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index 7a2adf402..7a8630ae2 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index b49815b72..82aeefbdf 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index 0d393cf35..cb077068b 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index bd3daccee..c64f3a11c 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index 565a25353..8263598f7 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index cd9404752..6131a793c 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index 29fb7db6d..8a6d23759 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index 3af52e155..e6c5b555b 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index 155b2a027..a27f03195 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index e645970aa..c51c6a6d0 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index 0bd24a2b9..647d3d6a1 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index d2fcbbea6..fd5563bc6 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index 9c99d1226..f3b949255 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index 1e3cf0496..408ee0e03 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index ec4cb42d3..62b3dc9a1 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index a67a8a203..7ed9e0f1c 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index 2821ee9fe..86b8a5f2e 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index 323365011..fd897c1de 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index ac0f4c36a..a366a6b74 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index 79d30bc7e..06031a95d 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index 654b42928..2cc552d94 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -63,5 +63,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index e74f889cf..1f1efdab8 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index 1738381bb..08217906d 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index bce8bdfae..f365e5f87 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index a8a09e929..3fb0b297e 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index 699fc11fb..108f9f02c 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config index 2cf558d76..ac1349689 100644 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ b/subworkflows/ncbigenomedownload/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index 9f579c331..05310aa3d 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index 3068f6a45..fa636bb63 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index e4de2406d..1db2e58ab 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index 71ee10dc6..668fb4e09 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index b32eced83..1f6233515 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index 3a04d38b2..721a4699a 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index b1857a810..5cc40eee6 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index 580b47d87..f3211cad1 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index 655317f7c..1b9e2a7f2 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index 3510bee1d..22a2910b7 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index b08628c4d..7df35a97e 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index c91bf8824..52dbf4f11 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index 9f26b9b56..044def318 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index 3afa08bec..c1575d983 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 1ca62e440..15090dccc 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index 3d7805866..19947e67a 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index 91dcc5ae3..cb95a8941 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -46,5 +46,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index df2e7b024..158984964 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 3ec269020..129bf2a29 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index 2b7bc37a1..d0d5cac40 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index 505d5582f..5d0e1c6f3 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index 2b4145053..a38c44a1d 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index 7e52406af..0d69bfef8 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index 834ada652..e94ead606 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -39,5 +39,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index f317c41f5..ed98a2763 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index 5e01e9e4b..1fb43f0e4 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index e8fa674fa..74b8ed4e1 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index a5f6ff5d3..99a5aba5e 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index ee7e31b47..f1d8067d2 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index d1b15d848..d252d47cb 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/staphscan/tests/nextflow.config b/subworkflows/staphscan/tests/nextflow.config index 43a008a0b..73cb8ff34 100644 --- a/subworkflows/staphscan/tests/nextflow.config +++ b/subworkflows/staphscan/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 0c96eadde..4769136ff 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index ee1ce74bb..ee46b7d88 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index a7193ad2b..d6f2574ea 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index ecec1d6c5..51bcf0660 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index 2a31dc2f0..5f5572cc9 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index 4b1d44ee5..709d8405d 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index ba4b5747d..97752aef6 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -42,5 +42,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/subworkflows/traitar/tests/nextflow.config b/subworkflows/traitar/tests/nextflow.config index 67649c816..94afb1059 100644 --- a/subworkflows/traitar/tests/nextflow.config +++ b/subworkflows/traitar/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index 35bf46b5d..22655cfb8 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index aef8ea97b..3c40c2320 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index 02939f490..c1d7843c0 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index f351fba1e..cca4b9f6a 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index f8cce8180..8e8814da5 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 26d7e8a00..452579c13 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index dd202ec2f..d491c5ddd 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 4d455d00c..88b6a49ef 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 64f3ac375..13d5d6216 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 9f6cb3693..1b77fa2b4 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index b34f325ff..f56570341 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index 548aa6f60..17117f07e 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index 0e019cb1a..6dffa0c0a 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 567c3dffc..a24e4c99a 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index 528e9a12b..d597a06b1 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 05d188ea7..4f0069459 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 57a54e004..952082bed 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index 0cf0e4ed7..e3a7e51f4 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index 9e29ea10f..bed0efd6a 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index ac1f67c50..5668ca4d1 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index daf219628..92c4bad96 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index c6f604bd6..996226c4e 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index 14730fb42..f3689bba2 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index ed6e22b79..e990779a6 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index 97b528093..4db50b44d 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index 753c5d750..ed750199d 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 63a4aa00d..24eaa8f5c 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index aad4766d5..5a0efb96e 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index 3944eb428..1d8f4d64d 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 13beac617..7dc154bd4 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index c0f74dfcb..fc8fd3cae 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index ae161e24a..a30fc519b 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 7168892fe..efcbcd172 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index bdd6c5ed4..0772454fa 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index aa2e0359a..12941931e 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index 7e10bdbf7..b0cd5cdba 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -111,7 +111,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index 5b8b24bbd..da7be08f6 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index fd7d513fa..9700fbfe3 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index 78deafdce..e052f04da 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index f3027b08a..0b728a170 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 781b9b147..b39f5d9b3 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index f545cf08e..351af9b1d 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index 1231f73f5..ef8efc78d 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index 60155a7b5..f58d55df9 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index 55c84a89c..c1c9ba8e3 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index c19255968..5cf667a1c 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index fa0acafa9..ff2fd53c1 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index dfb2226f5..11fe5bc9a 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 7db17a2be..7658c2c31 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index 4b3dc8b25..e32e5c12e 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index 774bbdd34..214bdbf3a 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index 5983eef1f..1b7fd5575 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -88,9 +88,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index aef16337b..234060022 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index 1a6d53456..fecfc548a 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 2ccb59552..6b0bfefec 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 2015cf435..c9e2192c1 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 9a078f9b8..50148fd0e 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index 7fc974733..bf96b8b9b 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 73f5ae3a8..09c0db53b 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index 97cd8ccc9..840b87364 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index bcd48c8d6..07166edc6 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index 7a33dad20..e294cb45a 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 36359167b..d01e7ebd9 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index 741a0d361..3f23b1984 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index e9254b0f1..6dba74008 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index f68946d8c..2dbbee43a 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index ba20328fa..1c4b41e67 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 9e4ebf1a5..52b73169b 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index 0b40bb3e4..ce9adc058 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index de251a32c..ae273982e 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -92,9 +92,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 6d18a57d9..6d78ccb0b 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -98,7 +98,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 6d1ad9e5e..977d39f57 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -94,9 +94,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.4' + id 'nf-bactopia@2.1.5' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} From 0d98787cf71feb52f834b7fdee1c6b36aa04ddb1 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 8 May 2026 11:54:18 -0600 Subject: [PATCH 12/43] bump version in bactopia wrapper --- bin/bactopia | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/bactopia b/bin/bactopia index dff17ac73..f6d4bab37 100755 --- a/bin/bactopia +++ b/bin/bactopia @@ -1,5 +1,5 @@ #!/usr/bin/env bash -VERSION=4.0.0 +VERSION=4.0.1 CONDA_ENV=$(which bactopia | sed 's=bin/bactopia==') BACTOPIA_NF="${CONDA_ENV}/share/bactopia-${VERSION}" From 67a3086d09ad83fd411360c85f7fd28f0e0bf5e6 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 8 May 2026 22:32:57 -0600 Subject: [PATCH 13/43] bump bactopia-py depend --- data/conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index ae1415469..532e96dc4 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -17,7 +17,7 @@ requirements: - python >3.9,<3.14 - wget run: - - bactopia-py >=2.1.6 + - bactopia-py >=2.2.0 - conda >=25 - coreutils - mamba >=2 From 795fd46e6cde1f8343bf785011a1902e0fda26a3 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 11 May 2026 21:02:16 -0600 Subject: [PATCH 14/43] bump plugin version --- nextflow.config | 2 +- subworkflows/abricate/tests/nextflow.config | 2 +- subworkflows/abritamr/tests/nextflow.config | 2 +- subworkflows/agrvate/tests/nextflow.config | 2 +- subworkflows/amrfinderplus/tests/nextflow.config | 2 +- subworkflows/ariba/tests/nextflow.config | 2 +- subworkflows/bactopia/assembler/tests/nextflow.config | 2 +- subworkflows/bactopia/qc/tests/nextflow.config | 2 +- subworkflows/bactopia/sketcher/tests/nextflow.config | 2 +- subworkflows/bakta/tests/nextflow.config | 2 +- subworkflows/blastn/tests/nextflow.config | 2 +- subworkflows/blastp/tests/nextflow.config | 2 +- subworkflows/blastx/tests/nextflow.config | 2 +- subworkflows/bracken/tests/nextflow.config | 2 +- subworkflows/btyper3/tests/nextflow.config | 2 +- subworkflows/busco/tests/nextflow.config | 2 +- subworkflows/checkm/tests/nextflow.config | 2 +- subworkflows/checkm2/tests/nextflow.config | 2 +- subworkflows/clermontyping/tests/nextflow.config | 2 +- subworkflows/clonalframeml/tests/nextflow.config | 2 +- subworkflows/deacon/tests/nextflow.config | 2 +- subworkflows/defensefinder/tests/nextflow.config | 2 +- subworkflows/ectyper/tests/nextflow.config | 2 +- subworkflows/eggnog/tests/nextflow.config | 2 +- subworkflows/emmtyper/tests/nextflow.config | 2 +- subworkflows/fastani/tests/nextflow.config | 2 +- subworkflows/gamma/tests/nextflow.config | 2 +- subworkflows/genotyphi/tests/nextflow.config | 2 +- subworkflows/gigatyper/tests/nextflow.config | 2 +- subworkflows/gtdb/tests/nextflow.config | 2 +- subworkflows/gubbins/tests/nextflow.config | 2 +- subworkflows/hicap/tests/nextflow.config | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 2 +- subworkflows/iqtree/tests/nextflow.config | 2 +- subworkflows/ismapper/tests/nextflow.config | 2 +- subworkflows/kleborate/tests/nextflow.config | 2 +- subworkflows/kraken2/tests/nextflow.config | 2 +- subworkflows/legsta/tests/nextflow.config | 2 +- subworkflows/lissero/tests/nextflow.config | 2 +- subworkflows/mashdist/tests/nextflow.config | 2 +- subworkflows/mashtree/tests/nextflow.config | 2 +- subworkflows/mcroni/tests/nextflow.config | 2 +- subworkflows/meningotype/tests/nextflow.config | 2 +- subworkflows/merlin/tests/nextflow.config | 2 +- subworkflows/merlindist/tests/nextflow.config | 2 +- subworkflows/midas/tests/nextflow.config | 2 +- subworkflows/mlst/tests/nextflow.config | 2 +- subworkflows/mobsuite/tests/nextflow.config | 2 +- subworkflows/mykrobe/tests/nextflow.config | 2 +- subworkflows/ncbigenomedownload/tests/nextflow.config | 2 +- subworkflows/ngmaster/tests/nextflow.config | 2 +- subworkflows/nohuman/tests/nextflow.config | 2 +- subworkflows/panaroo/tests/nextflow.config | 2 +- subworkflows/pangenome/tests/nextflow.config | 2 +- subworkflows/pasty/tests/nextflow.config | 2 +- subworkflows/pbptyper/tests/nextflow.config | 2 +- subworkflows/phispy/tests/nextflow.config | 2 +- subworkflows/pirate/tests/nextflow.config | 2 +- subworkflows/plasmidfinder/tests/nextflow.config | 2 +- subworkflows/pneumocat/tests/nextflow.config | 2 +- subworkflows/prokka/tests/nextflow.config | 2 +- subworkflows/quast/tests/nextflow.config | 2 +- subworkflows/rgi/tests/nextflow.config | 2 +- subworkflows/roary/tests/nextflow.config | 2 +- subworkflows/sccmec/tests/nextflow.config | 2 +- subworkflows/scoary/tests/nextflow.config | 2 +- subworkflows/scrubber/tests/nextflow.config | 2 +- subworkflows/seqsero2/tests/nextflow.config | 2 +- subworkflows/seroba/tests/nextflow.config | 2 +- subworkflows/shigapass/tests/nextflow.config | 2 +- subworkflows/shigatyper/tests/nextflow.config | 2 +- subworkflows/shigeifinder/tests/nextflow.config | 2 +- subworkflows/sistr/tests/nextflow.config | 2 +- subworkflows/snippy/core/tests/nextflow.config | 2 +- subworkflows/snippy/run/tests/nextflow.config | 2 +- subworkflows/snpdists/tests/nextflow.config | 2 +- subworkflows/spatyper/tests/nextflow.config | 2 +- subworkflows/srahumanscrubber/tests/nextflow.config | 2 +- subworkflows/ssuissero/tests/nextflow.config | 2 +- subworkflows/staphopiasccmec/tests/nextflow.config | 2 +- subworkflows/staphscan/tests/nextflow.config | 2 +- subworkflows/staphtyper/tests/nextflow.config | 2 +- subworkflows/stecfinder/tests/nextflow.config | 2 +- subworkflows/sylph/tests/nextflow.config | 2 +- subworkflows/tblastn/tests/nextflow.config | 2 +- subworkflows/tblastx/tests/nextflow.config | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 2 +- subworkflows/teton/tests/nextflow.config | 2 +- subworkflows/traitar/tests/nextflow.config | 2 +- workflows/bactopia-tools/abricate/nextflow.config | 2 +- workflows/bactopia-tools/abritamr/nextflow.config | 2 +- workflows/bactopia-tools/agrvate/nextflow.config | 2 +- workflows/bactopia-tools/amrfinderplus/nextflow.config | 2 +- workflows/bactopia-tools/ariba/nextflow.config | 2 +- workflows/bactopia-tools/bakta/nextflow.config | 2 +- workflows/bactopia-tools/blastn/nextflow.config | 2 +- workflows/bactopia-tools/blastp/nextflow.config | 2 +- workflows/bactopia-tools/blastx/nextflow.config | 2 +- workflows/bactopia-tools/bracken/nextflow.config | 2 +- workflows/bactopia-tools/btyper3/nextflow.config | 2 +- workflows/bactopia-tools/busco/nextflow.config | 2 +- workflows/bactopia-tools/checkm/nextflow.config | 2 +- workflows/bactopia-tools/checkm2/nextflow.config | 2 +- workflows/bactopia-tools/clermontyping/nextflow.config | 2 +- workflows/bactopia-tools/defensefinder/nextflow.config | 2 +- workflows/bactopia-tools/ectyper/nextflow.config | 2 +- workflows/bactopia-tools/eggnog/nextflow.config | 2 +- workflows/bactopia-tools/emmtyper/nextflow.config | 2 +- workflows/bactopia-tools/fastani/nextflow.config | 2 +- workflows/bactopia-tools/gamma/nextflow.config | 2 +- workflows/bactopia-tools/genotyphi/nextflow.config | 2 +- workflows/bactopia-tools/gigatyper/nextflow.config | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 2 +- workflows/bactopia-tools/hicap/nextflow.config | 2 +- workflows/bactopia-tools/hpsuissero/nextflow.config | 2 +- workflows/bactopia-tools/ismapper/nextflow.config | 2 +- workflows/bactopia-tools/kleborate/nextflow.config | 2 +- workflows/bactopia-tools/kraken2/nextflow.config | 2 +- workflows/bactopia-tools/legsta/nextflow.config | 2 +- workflows/bactopia-tools/lissero/nextflow.config | 2 +- workflows/bactopia-tools/mashdist/nextflow.config | 2 +- workflows/bactopia-tools/mashtree/nextflow.config | 2 +- workflows/bactopia-tools/mcroni/nextflow.config | 2 +- workflows/bactopia-tools/meningotype/nextflow.config | 2 +- workflows/bactopia-tools/merlin/nextflow.config | 2 +- workflows/bactopia-tools/midas/nextflow.config | 2 +- workflows/bactopia-tools/mlst/nextflow.config | 2 +- workflows/bactopia-tools/mobsuite/nextflow.config | 2 +- workflows/bactopia-tools/mykrobe/nextflow.config | 2 +- workflows/bactopia-tools/ngmaster/nextflow.config | 2 +- workflows/bactopia-tools/pangenome/nextflow.config | 2 +- workflows/bactopia-tools/pasty/nextflow.config | 2 +- workflows/bactopia-tools/pbptyper/nextflow.config | 2 +- workflows/bactopia-tools/phispy/nextflow.config | 2 +- workflows/bactopia-tools/plasmidfinder/nextflow.config | 2 +- workflows/bactopia-tools/pneumocat/nextflow.config | 2 +- workflows/bactopia-tools/prokka/nextflow.config | 2 +- workflows/bactopia-tools/quast/nextflow.config | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 2 +- workflows/bactopia-tools/sccmec/nextflow.config | 2 +- workflows/bactopia-tools/scrubber/nextflow.config | 2 +- workflows/bactopia-tools/seqsero2/nextflow.config | 2 +- workflows/bactopia-tools/seroba/nextflow.config | 2 +- workflows/bactopia-tools/shigapass/nextflow.config | 2 +- workflows/bactopia-tools/shigatyper/nextflow.config | 2 +- workflows/bactopia-tools/shigeifinder/nextflow.config | 2 +- workflows/bactopia-tools/sistr/nextflow.config | 2 +- workflows/bactopia-tools/snippy/nextflow.config | 2 +- workflows/bactopia-tools/spatyper/nextflow.config | 2 +- workflows/bactopia-tools/ssuissero/nextflow.config | 2 +- workflows/bactopia-tools/staphscan/nextflow.config | 2 +- workflows/bactopia-tools/staphtyper/nextflow.config | 2 +- workflows/bactopia-tools/stecfinder/nextflow.config | 2 +- workflows/bactopia-tools/sylph/nextflow.config | 2 +- workflows/bactopia-tools/tblastn/nextflow.config | 2 +- workflows/bactopia-tools/tblastx/nextflow.config | 2 +- workflows/bactopia-tools/tbprofiler/nextflow.config | 2 +- workflows/bactopia-tools/traitar/nextflow.config | 2 +- workflows/cleanyerreads/nextflow.config | 2 +- workflows/staphopia/nextflow.config | 2 +- workflows/teton/nextflow.config | 2 +- 161 files changed, 161 insertions(+), 161 deletions(-) diff --git a/nextflow.config b/nextflow.config index c960c3541..58a772fbd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -118,7 +118,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index 62e8b1ea3..829218003 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index 025ce8d51..7681f58b4 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index 5bfc14a35..1ebdea255 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index f15694d24..5042cf02a 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index 753ec333b..5e44ac983 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index 93bd49596..4d89e7ac3 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -67,5 +67,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index 3855a1308..a89cb2fa5 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -73,5 +73,5 @@ includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index 15cda5354..882fb3df0 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index f21f9249c..40001ff16 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index 14ddb6c9d..b2347317e 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index 05f1580b2..72c82e788 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index e88bbb9bd..107e76f54 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index c75a26018..1fc6e966f 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index 01c023876..c4ce1f7a8 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index ef6601e60..ec93f2248 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index 27ad7278c..b29827030 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index aa1884f34..1b025f6fe 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index 4db815d33..faa6a2663 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index 0f096fd57..1f021ec7d 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/deacon/tests/nextflow.config b/subworkflows/deacon/tests/nextflow.config index 76bafcd79..6c503aa7c 100644 --- a/subworkflows/deacon/tests/nextflow.config +++ b/subworkflows/deacon/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index 7d6adc872..c6ed1717c 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index 8350a5e2a..6c2cedd63 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index 7a8630ae2..7dc7f4bce 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index 82aeefbdf..b67bb3859 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index cb077068b..d7ebb8a78 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index c64f3a11c..6969b68d1 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index 8263598f7..1052e746f 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index 6131a793c..dfa06e727 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index 8a6d23759..2d309645d 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index e6c5b555b..fa5f53203 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index a27f03195..d8f4001f9 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index c51c6a6d0..15c812a44 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index 647d3d6a1..da69c602a 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index fd5563bc6..a1c26e792 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index f3b949255..77231e301 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index 408ee0e03..e7805dd59 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index 62b3dc9a1..9c3349558 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index 7ed9e0f1c..3fc4be87f 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index 86b8a5f2e..58a3ca1b9 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index fd897c1de..1fa446447 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index a366a6b74..92b46f267 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index 06031a95d..81ff41fac 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index 2cc552d94..80e6ecbcf 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -63,5 +63,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index 1f1efdab8..4ac50872b 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index 08217906d..e06173209 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index f365e5f87..6611b68e8 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index 3fb0b297e..1467a0187 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index 108f9f02c..92c25d53c 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config index ac1349689..9ae560ede 100644 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ b/subworkflows/ncbigenomedownload/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index 05310aa3d..6deafb497 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index fa636bb63..03c7bcc1f 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index 1db2e58ab..e07577ef5 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index 668fb4e09..8dbc7a04f 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index 1f6233515..3a233617e 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index 721a4699a..d9c0c9ddc 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index 5cc40eee6..e19e5a2d8 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index f3211cad1..50c2dd390 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index 1b9e2a7f2..54d0b2e67 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index 22a2910b7..3626afe48 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index 7df35a97e..153eae26c 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index 52dbf4f11..4726b4414 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index 044def318..5b1c2eeeb 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index c1575d983..0fe2597e7 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 15090dccc..63fe4a812 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index 19947e67a..5145b6a80 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index cb95a8941..a0db097db 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -46,5 +46,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index 158984964..2b625e033 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 129bf2a29..19fe2d42f 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index d0d5cac40..55ee50fda 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index 5d0e1c6f3..6902b7330 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index a38c44a1d..6a508232d 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index 0d69bfef8..3c684a198 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index e94ead606..e42a5908d 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -39,5 +39,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index ed98a2763..3e48f2928 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index 1fb43f0e4..ae6f1e29d 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -35,5 +35,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index 74b8ed4e1..440532f20 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index 99a5aba5e..0e7e0a23e 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index f1d8067d2..e39af0057 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index d252d47cb..3ec5964fc 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/staphscan/tests/nextflow.config b/subworkflows/staphscan/tests/nextflow.config index 73cb8ff34..295dacfea 100644 --- a/subworkflows/staphscan/tests/nextflow.config +++ b/subworkflows/staphscan/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 4769136ff..8c199ac95 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -38,5 +38,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index ee46b7d88..4ac09faf4 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index d6f2574ea..6f0473312 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index 51bcf0660..c143cad0f 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index 5f5572cc9..322989a22 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index 709d8405d..db03f2105 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -36,5 +36,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index 97752aef6..c870f0b33 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -42,5 +42,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/subworkflows/traitar/tests/nextflow.config b/subworkflows/traitar/tests/nextflow.config index 94afb1059..72b376705 100644 --- a/subworkflows/traitar/tests/nextflow.config +++ b/subworkflows/traitar/tests/nextflow.config @@ -37,5 +37,5 @@ includeConfig "../../../conf/profiles.config" // Plugin plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index 22655cfb8..5c17ed5e2 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 3c40c2320..0723f02b2 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index c1d7843c0..accab6c24 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index cca4b9f6a..f8ed3bf45 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index 8e8814da5..98fd0e4b9 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 452579c13..405a16ffe 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index d491c5ddd..5224360b4 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 88b6a49ef..87cd40c7c 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 13d5d6216..b00135147 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 1b77fa2b4..cc671fbe1 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index f56570341..30c7957bc 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index 17117f07e..f7213715b 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index 6dffa0c0a..4f64f7a21 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index a24e4c99a..79771ed5d 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index d597a06b1..d459b8145 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 4f0069459..bfe8f90e8 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 952082bed..69b20ef12 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index e3a7e51f4..16dbdf394 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index bed0efd6a..d4d845927 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index 5668ca4d1..982fbddce 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index 92c4bad96..fab2ece18 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index 996226c4e..0a4699400 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index f3689bba2..0f0bf0302 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index e990779a6..b3c5e9737 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index 4db50b44d..ccf0cbf73 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index ed750199d..c46376282 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 24eaa8f5c..3a2019366 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index 5a0efb96e..5dc25af71 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index 1d8f4d64d..e85ecf0ae 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 7dc154bd4..bd5a68d94 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index fc8fd3cae..97e6ac23a 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index a30fc519b..b4cefb47f 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index efcbcd172..151cca771 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 0772454fa..ade53db3e 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index 12941931e..0c1d8f1ff 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index b0cd5cdba..a826d2996 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -111,7 +111,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index da7be08f6..301b33fe0 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index 9700fbfe3..6901330ea 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index e052f04da..93ba6d3bf 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index 0b728a170..8bc658a00 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index b39f5d9b3..5e873074b 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index 351af9b1d..a8476c710 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index ef8efc78d..37243b1fd 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index f58d55df9..12421f574 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index c1c9ba8e3..38ccbba70 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 5cf667a1c..3ea635a51 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index ff2fd53c1..97395f464 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index 11fe5bc9a..cc96db7b8 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -82,7 +82,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 7658c2c31..4efd351fe 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index e32e5c12e..cb0624296 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index 214bdbf3a..a98c88393 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index 1b7fd5575..3cae14963 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -88,7 +88,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index 234060022..323206894 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index fecfc548a..6124b6639 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 6b0bfefec..67def7e3d 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index c9e2192c1..acab21ce7 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 50148fd0e..2477af508 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index bf96b8b9b..cb29ec1fd 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 09c0db53b..10309a4ef 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index 840b87364..479a0f8b9 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 07166edc6..3fd2bde6e 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index e294cb45a..bbfd45818 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index d01e7ebd9..cb945184e 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index 3f23b1984..3bbd78b12 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 6dba74008..4460026eb 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index 2dbbee43a..aec6f670c 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 1c4b41e67..6d16650c6 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 52b73169b..5778e21b9 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -83,7 +83,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index ce9adc058..f0e42e9e6 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -84,7 +84,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index ae273982e..e0bfcc125 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -92,7 +92,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 6d78ccb0b..f5ad70e5d 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -98,7 +98,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 977d39f57..7e27d77ac 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -94,7 +94,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { From f3b6fabd3f13eca298f5bd07699bb700c38c92b3 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 16 May 2026 07:16:05 -0600 Subject: [PATCH 15/43] set genomesize to 0 in cleanyerreads and teton configs --- .vscode/settings.json | 22 +++++++++++++++++++ CHANGELOG.md | 2 ++ catalog.json | 2 +- conf/base.config | 2 +- conf/params/cleanyerreads.config | 2 +- conf/params/teton.config | 2 +- main.nf | 4 +++- modules/bactopia/gather/module.config | 6 ++--- .../bactopia/gather/schema-cleanyerreads.json | 2 +- 9 files changed, 35 insertions(+), 9 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index ef4fefcc7..69f4e8d57 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -52,6 +52,7 @@ "ariba", "Arkin", "Armbrust", + "aspera", "Astashyn", "Avagyan", "awsbatch", @@ -96,6 +97,7 @@ "bioperl", "Biosequence", "Biotechnol", + "biotools", "Birney", "bitscore", "blastdb", @@ -127,6 +129,7 @@ "btype", "BTYPER", "Buchfink", + "Burnedead's", "busco", "Busó", "bwaopt", @@ -184,6 +187,7 @@ "contigs", "contree", "Corander", + "coreutils", "Cosentino", "Coulouris", "cpus", @@ -336,6 +340,7 @@ "Grabysz", "Griffiths", "Griswold", + "groovydoc", "Gruber", "gsize", "gtdb", @@ -430,6 +435,7 @@ "Kaufmann", "Kaur", "Keane", + "keepfiles", "KEGG", "Kempf", "Kimelman", @@ -482,6 +488,7 @@ "lipopolysaccharide", "lissero", "Litt", + "llms", "locustag", "Lohse", "lowmem", @@ -496,6 +503,7 @@ "Maguire", "Mahé", "makeblastdb", + "makedb", "Mallonee", "mambaforge", "Manni", @@ -504,6 +512,7 @@ "Marth", "mashdist", "mashtree", + "maskmiddle", "maskrc", "Masterson", "Mathys", @@ -511,6 +520,7 @@ "maxcor", "maxhap", "maxlcummins", + "maxlength", "maxsoft", "mccortex", "mcroni", @@ -532,6 +542,7 @@ "metagenomes", "metagenomic", "metagenomics", + "Metamorph", "methicillin", "Microb", "Microbiol", @@ -545,10 +556,13 @@ "miniasm", "minid", "Miniforge", + "minlen", "minlength", "Minm", "minmer", "minqual", + "minquality", + "minreadlen", "minscore", "Miroshnichenko", "misassembly", @@ -620,19 +634,24 @@ "nonprophage", "nopath", "noplus", + "nopolish", + "noreadcorr", "noreorient", "nosetests", + "nostitch", "Notredame", "nthi", "ntmax", "nucl", "nucmer", + "nullifybrokenquality", "numcpus", "Nurk", "Ohan", "Oloni", "Ondov", "opcov", + "openpyxl", "opid", "Oppong", "ords", @@ -701,6 +720,7 @@ "pneumocat", "pneumoniae", "pneumophila", + "polypolish", "pora", "porb", "porechop", @@ -862,6 +882,7 @@ "skesa", "sketchsize", "Slotta", + "SLURM", "SNPDISTS", "snpeff", "snpsites", @@ -937,6 +958,7 @@ "Tomita", "Tommaso", "Tonder", + "tossbrokenreads", "tossjunk", "Touchon", "Traitar", diff --git a/CHANGELOG.md b/CHANGELOG.md index 39b4272a1..44531250f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,8 @@ sidebar_position: 5000 - Deacon as the default host read scrubber (replaces nohuman as default) - Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules - Three-way scrubber selection: deacon (default), nohuman (`--use_nohuman`), SRA Human Scrubber (`--use_srascrubber`) +- Bump internal bactopia-* pipeline tool versions + - `bactopia-gather`: 1.0.5 -> 1.0.6 ### `Changed` diff --git a/catalog.json b/catalog.json index 8915088d2..aa6f59e61 100644 --- a/catalog.json +++ b/catalog.json @@ -299,7 +299,7 @@ "process_name": "gather", "tool": { "name": "bactopia-gather", - "version": "1.0.5" + "version": "1.0.6" }, "takes": [ "r1_files", diff --git a/conf/base.config b/conf/base.config index 22153b882..aa1326ce7 100644 --- a/conf/base.config +++ b/conf/base.config @@ -52,7 +52,7 @@ process { time = { 96.h * task.attempt } } withLabel: process_high_memory { - memory = { 128.GB * task.attempt } + memory = { 144.GB * task.attempt } } withLabel: error_ignore { errorStrategy = 'ignore' diff --git a/conf/params/cleanyerreads.config b/conf/params/cleanyerreads.config index 17188b256..51b790c4b 100644 --- a/conf/params/cleanyerreads.config +++ b/conf/params/cleanyerreads.config @@ -11,7 +11,7 @@ params { // Optional Parameters coverage = 0 - genome_size = "1" + genome_size = 0 // Gather Samples Parameters enable_fastq_check = false diff --git a/conf/params/teton.config b/conf/params/teton.config index 82fe0adfb..e6c821c73 100644 --- a/conf/params/teton.config +++ b/conf/params/teton.config @@ -8,7 +8,7 @@ params { // Optional Parameters coverage = 0 - genome_size = "1" + genome_size = 0 sampleseed = 42 // Kraken2 Parameters diff --git a/main.nf b/main.nf index 0aa9bb9d5..cc91dcbcf 100644 --- a/main.nf +++ b/main.nf @@ -161,6 +161,7 @@ params { ask_merlin : Boolean spatyper_repeats : Path? spatyper_repeat_order : Path? + staphscan_db_mlst : Path? } // Core @@ -260,7 +261,8 @@ workflow { params.hicap_model_fp, // staphtyper params.spatyper_repeats, - params.spatyper_repeat_order + params.spatyper_repeat_order, + params.staphscan_db_mlst ) ch_sample_outputs = ch_sample_outputs.mix(ch_merlin.sample_outputs) ch_run_outputs = ch_run_outputs.mix(ch_merlin.run_outputs) diff --git a/modules/bactopia/gather/module.config b/modules/bactopia/gather/module.config index 658d68c99..5b00cccb3 100644 --- a/modules/bactopia/gather/module.config +++ b/modules/bactopia/gather/module.config @@ -24,9 +24,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::bactopia-gather=1.0.5".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-gather:1.0.5--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-gather:1.0.5--hdfd78af_0" + ext.toolName = "bioconda::bactopia-gather=1.1.1".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-gather:1.1.1--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-gather:1.1.1--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/bactopia/gather/schema-cleanyerreads.json b/modules/bactopia/gather/schema-cleanyerreads.json index 5780345be..68e7cbd9b 100644 --- a/modules/bactopia/gather/schema-cleanyerreads.json +++ b/modules/bactopia/gather/schema-cleanyerreads.json @@ -27,7 +27,7 @@ }, "genome_size": { "type": "string", - "default": "1", + "default": "0", "description": "Expected genome size (bp) for all samples", "help": "If `--species` is used, `min`, `median`, `mean`, or `max` can be used for `--genome_size`", "fa_icon": "fas fa-arrows-alt-h", From 6db6e2cbe420b95e92c84469fd8eda850cd7f1a2 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 16 May 2026 07:23:15 -0600 Subject: [PATCH 16/43] gha updates --- .github/workflows/conda-build-manual.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/conda-build-manual.yml b/.github/workflows/conda-build-manual.yml index bf127d82d..81ec75e20 100644 --- a/.github/workflows/conda-build-manual.yml +++ b/.github/workflows/conda-build-manual.yml @@ -16,7 +16,7 @@ jobs: ref: dev - name: Setup Miniforge - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: activate-environment: anaconda-client-env conda-remove-defaults: "true" From 7f715e87706e70a9a7358912ff790b93424ba736 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 16 May 2026 07:26:48 -0600 Subject: [PATCH 17/43] gha excitement --- .github/workflows/conda-build-manual.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/conda-build-manual.yml b/.github/workflows/conda-build-manual.yml index 81ec75e20..bab8bd2ec 100644 --- a/.github/workflows/conda-build-manual.yml +++ b/.github/workflows/conda-build-manual.yml @@ -26,7 +26,7 @@ jobs: run: | # Start build conda install -c conda-forge -c bioconda anaconda-client conda-build conda-verify - cd data/conda/ && conda build -c conda-forge -c bioconda --output-folder . . + cd data/conda/ && conda-build -c conda-forge -c bioconda --output-folder . . anaconda upload --force ./noarch/*.conda env: ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} From 4a4c8da4c03447b6c4dac6e0cc5d7c8030de318f Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Thu, 21 May 2026 14:02:04 -0600 Subject: [PATCH 18/43] add stxtyper as a bactopia-tool --- catalog.json | 73 ++- data/citations.yml | 7 + llms.txt | 4 +- modules/stxtyper/main.nf | 84 ++++ modules/stxtyper/module.config | 23 + modules/stxtyper/schema.json | 23 + modules/stxtyper/tests/main.nf.test | 37 ++ modules/stxtyper/tests/main.nf.test.snap | 23 + modules/stxtyper/tests/nextflow.config | 36 ++ modules/stxtyper/tests/nf-test.config | 11 + subworkflows/stxtyper/main.nf | 43 ++ subworkflows/stxtyper/tests/.nftignore | 2 + subworkflows/stxtyper/tests/main.nf.test | 45 ++ subworkflows/stxtyper/tests/main.nf.test.snap | 34 ++ subworkflows/stxtyper/tests/nextflow.config | 40 ++ subworkflows/stxtyper/tests/nf-test.config | 11 + workflows/bactopia-tools/stxtyper/main.nf | 78 ++++ .../bactopia-tools/stxtyper/nextflow.config | 91 ++++ .../stxtyper/nextflow_schema.json | 429 ++++++++++++++++++ .../bactopia-tools/stxtyper/tests/.nftignore | 3 + .../stxtyper/tests/main.nf.test | 43 ++ .../stxtyper/tests/main.nf.test.snap | 51 +++ .../stxtyper/tests/nf-test.config | 11 + 23 files changed, 1196 insertions(+), 6 deletions(-) create mode 100644 modules/stxtyper/main.nf create mode 100644 modules/stxtyper/module.config create mode 100644 modules/stxtyper/schema.json create mode 100644 modules/stxtyper/tests/main.nf.test create mode 100644 modules/stxtyper/tests/main.nf.test.snap create mode 100644 modules/stxtyper/tests/nextflow.config create mode 100644 modules/stxtyper/tests/nf-test.config create mode 100644 subworkflows/stxtyper/main.nf create mode 100644 subworkflows/stxtyper/tests/.nftignore create mode 100644 subworkflows/stxtyper/tests/main.nf.test create mode 100644 subworkflows/stxtyper/tests/main.nf.test.snap create mode 100644 subworkflows/stxtyper/tests/nextflow.config create mode 100644 subworkflows/stxtyper/tests/nf-test.config create mode 100644 workflows/bactopia-tools/stxtyper/main.nf create mode 100644 workflows/bactopia-tools/stxtyper/nextflow.config create mode 100644 workflows/bactopia-tools/stxtyper/nextflow_schema.json create mode 100644 workflows/bactopia-tools/stxtyper/tests/.nftignore create mode 100644 workflows/bactopia-tools/stxtyper/tests/main.nf.test create mode 100644 workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap create mode 100644 workflows/bactopia-tools/stxtyper/tests/nf-test.config diff --git a/catalog.json b/catalog.json index aa6f59e61..bcce89d59 100644 --- a/catalog.json +++ b/catalog.json @@ -1,9 +1,9 @@ { "version": "1.0", - "generated": "2026-05-06T20:36:40Z", + "generated": "2026-05-21T19:57:48Z", "bactopia_version": "4.0.1", - "bactopia_py_version": "2.1.6", - "nf_bactopia_version": "2.1.5", + "bactopia_py_version": "2.2.0", + "nf_bactopia_version": "2.1.6", "modules": { "abricate_run": { "description": "Mass screening of contigs for antimicrobial and virulence genes.", @@ -299,7 +299,7 @@ "process_name": "gather", "tool": { "name": "bactopia-gather", - "version": "1.0.6" + "version": "1.1.1" }, "takes": [ "r1_files", @@ -2917,6 +2917,30 @@ ] } }, + "stxtyper": { + "description": "Identify and type Stx operons from assembled genomic sequences", + "path": "modules/stxtyper/", + "scope": "sample", + "process_name": "stxtyper", + "tool": { + "name": "ncbi-stxtyper", + "version": "1.0.45" + }, + "takes": [ + "fna" + ], + "emits": [ + "tsv" + ], + "tags": { + "complexity": "simple", + "input_type": "single", + "output_type": "single", + "features": [ + "conditional-logic" + ] + } + }, "sylph_profile": { "description": "Profile metagenome samples against a database using Sylph.", "path": "modules/sylph/profile/", @@ -6209,6 +6233,36 @@ ] } }, + "stxtyper": { + "description": "Identify and type Stx operons from assembled genomic sequences", + "path": "subworkflows/stxtyper/", + "takes": [ + "fna" + ], + "emits": { + "sample_outputs": [ + "tsv" + ], + "run_outputs": [ + "csv" + ] + }, + "scope": "sample", + "calls": { + "modules": [ + "stxtyper", + "csvtk_concat" + ] + }, + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "aggregation" + ] + } + }, "sylph": { "description": "Profile microbial composition using Sylph.", "path": "subworkflows/sylph/", @@ -7184,6 +7238,17 @@ "stecfinder" ] }, + "stxtyper": { + "description": "Identify and type Stx operons from assembled genomic sequences", + "type": "tool", + "path": "workflows/bactopia-tools/stxtyper/", + "ext": [ + "fna" + ], + "subworkflows": [ + "stxtyper" + ] + }, "sylph": { "description": "Taxonomic profiling by abundance-corrected MinHash.", "type": "tool", diff --git a/data/citations.yml b/data/citations.yml index 843bf251c..3d949dc15 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -1066,6 +1066,13 @@ tools: cite: | Zhang X, Payne M, Kaur S, and Lan R [Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers.](https://doi.org/10.3389/fcimb.2021.772574) _Frontiers in Cellular and Infection Microbiology_, 11, 772574. (2021) + stxtyper: + name: StxTyper + link: https://github.com/ncbi/stxtyper + description: Identify and type Stx operons from assembled genomic sequences + cite: | + Feldgarden M, Brover V, Gonzalez-Escalona N, Frrat JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W [AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence.](https://doi.org/10.1038/s41598-021-91456-0) _Scientific Reports_ 11, 12728 (2021) + sylph: name: Sylph link: https://github.com/bluenote-1/sylph diff --git a/llms.txt b/llms.txt index a5dd7bba8..be1811c88 100644 --- a/llms.txt +++ b/llms.txt @@ -23,7 +23,7 @@ All components use standardized GroovyDoc documentation and static typing. - [workflows/cleanyerreads/](workflows/cleanyerreads/): Quality control and optional host read removal from raw sequencing reads. - [workflows/staphopia/](workflows/staphopia/): Comprehensive analysis pipeline for Staphylococcus aureus isolates. - [workflows/teton/](workflows/teton/): Taxonomic classification and abundance profiling of metagenomic reads. -- [workflows/bactopia-tools/](workflows/bactopia-tools/): 69 comparative analysis workflows (pan-genome, phylogenetics, typing) +- [workflows/bactopia-tools/](workflows/bactopia-tools/): 70 comparative analysis workflows (pan-genome, phylogenetics, typing) ## Subworkflows (Tier 2) @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -104 tool-specific modules live under `modules/`. Each module directory contains: +105 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/stxtyper/main.nf b/modules/stxtyper/main.nf new file mode 100644 index 000000000..30025e2d0 --- /dev/null +++ b/modules/stxtyper/main.nf @@ -0,0 +1,84 @@ +/** + * Identify and type Stx operons from assembled genomic sequences + * + * Uses [StxTyper](https://github.com/ncbi/stxtyper) to identify and type stx operons from assembled genomic sequences. + * + * @status stable + * @keywords stx, shiga toxin, typing, stec, virulence + * @tags complexity:simple input-type:single output-type:single features:conditional-logic + * @citation stxtyper + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @output record(meta, tsv, results, logs, nf_logs, versions) + * - `tsv`: Tab-delimited Stx operon typing results + */ +nextflow.enable.types = true + +process STXTYPER { + tag "${prefix}" + label 'process_low' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + record ( + meta: Record, + fna: Path + ) + + output: + record( + // Named fields (used downstream) + meta: meta, + tsv: file("${prefix}.tsv"), + // Generic fields (used for publishing) + results: [ + files("${prefix}.tsv") + ], + logs: files("*.{log,err}", optional: true), + nf_logs: files(".command.*"), + versions: files("versions.yml") + ) + + script: + def _meta = meta + prefix = task.ext.prefix ?: "${_meta.name}" + + // Create a new meta record + meta = record( + id: "${prefix}-${task.process}", + name: prefix, + scope: task.ext.scope, + output_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}", + logs_dir: "${prefix}/tools/${task.ext.process_name}/${task.ext.subdir}/logs/${task.ext.logs_subdir}", + process_name: task.ext.process_name + ) + + def is_compressed = fna.getName().endsWith(".gz") ? true : false + def fna_name = fna.getName().replace(".gz", "") + """ + if [ "${is_compressed}" == "true" ]; then + gzip -c -d ${fna} > ${fna_name} + fi + + stxtyper \\ + -n ${fna_name} \\ + --name ${prefix} \\ + ${task.ext.args} \\ + -o ${prefix}.tsv + + # Cleanup + if [ "${is_compressed}" == "true" ]; then + rm -rf ${fna_name} + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + stxtyper: \$( stxtyper --version 2>&1 ) + END_VERSIONS + """ +} diff --git a/modules/stxtyper/module.config b/modules/stxtyper/module.config new file mode 100644 index 000000000..84ab82fdd --- /dev/null +++ b/modules/stxtyper/module.config @@ -0,0 +1,23 @@ +params { + // stxtyper +} + +process { + withName: 'STXTYPER' { + ext.wf = params.wf + ext.scope = "sample" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "stxtyper" + + // Tool arguments + ext.args = [ + ].join(' ').replaceAll("\\s{2,}", " ").trim() + + // Environment information + ext.toolName = "bioconda::ncbi-stxtyper=1.0.45".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/ncbi-stxtyper:1.0.45--h9948957_0" + ext.image = "https://depot.galaxyproject.org/singularity/ncbi-stxtyper:1.0.45--h9948957_0" + ext.condaDir = "${params.condadir}" + } +} diff --git a/modules/stxtyper/schema.json b/modules/stxtyper/schema.json new file mode 100644 index 000000000..e9337f0a1 --- /dev/null +++ b/modules/stxtyper/schema.json @@ -0,0 +1,23 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/stxtyper/schema.json", + "title": "StxTyper Module", + "description": "A module for identify and type stx operons from assembled genomic sequences", + "type": "object", + "$defs": { + "stxtyper_parameters": { + "title": "StxTyper Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/stxtyper_parameters" + } + ] +} diff --git a/modules/stxtyper/tests/main.nf.test b/modules/stxtyper/tests/main.nf.test new file mode 100644 index 000000000..dd3e95f8d --- /dev/null +++ b/modules/stxtyper/tests/main.nf.test @@ -0,0 +1,37 @@ +nextflow_process { + name "Test STXTYPER" + script "../main.nf" + process "STXTYPER" + tag "modules" + tag "stxtyper" + + test("stxtyper - module - GCF_001695515") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_001695515"], + fna: file("${params.test_data_dir}/species/escherichia_coli/uncompressed/GCF_001695515/main/assembler/GCF_001695515.fna") + ) + ) + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.tsv, + record.versions + ).match() } + ) + } + } +} diff --git a/modules/stxtyper/tests/main.nf.test.snap b/modules/stxtyper/tests/main.nf.test.snap new file mode 100644 index 000000000..cbb4803c2 --- /dev/null +++ b/modules/stxtyper/tests/main.nf.test.snap @@ -0,0 +1,23 @@ +{ + "stxtyper - module - GCF_001695515": { + "content": [ + { + "id": "GCF_001695515-STXTYPER", + "logs_dir": "GCF_001695515/tools/stxtyper//logs/", + "name": "GCF_001695515", + "output_dir": "GCF_001695515/tools/stxtyper/", + "process_name": "stxtyper", + "scope": "sample" + }, + "GCF_001695515.tsv:md5,001feff7db6e3fad984fdc36327122cc", + [ + "versions.yml:md5,f9ebd9c1f28e4ce3da541f707abeaa52" + ] + ], + "timestamp": "2026-05-21T13:54:27.24411333", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/stxtyper/tests/nextflow.config b/modules/stxtyper/tests/nextflow.config new file mode 100644 index 000000000..ca3810ec1 --- /dev/null +++ b/modules/stxtyper/tests/nextflow.config @@ -0,0 +1,36 @@ +// Minimal config for module-level testing of STXTYPER +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "stxtyper" + logo_name = "bactopia-tools" + description = "Identify and type Stx operons from assembled genomic sequences" + ext = "fna" + } + + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +includeConfig "../module.config" +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" diff --git a/modules/stxtyper/tests/nf-test.config b/modules/stxtyper/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/modules/stxtyper/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/subworkflows/stxtyper/main.nf b/subworkflows/stxtyper/main.nf new file mode 100644 index 000000000..9a11d344d --- /dev/null +++ b/subworkflows/stxtyper/main.nf @@ -0,0 +1,43 @@ +/** + * Identify and type Stx operons from assembled genomic sequences + * + * This subworkflow uses [StxTyper](https://github.com/ncbi/stxtyper) to identify and type stx operons from assembled genomic sequences. + * It processes each sample individually and aggregates the results into + * a single consolidated report. + * + * @status stable + * @keywords stx, shiga toxin, typing, stec, virulence + * @tags complexity:moderate input-type:single output-type:multiple features:aggregation + * @citation stxtyper + * + * @modules csvtk_concat, stxtyper + * + * @input record(meta, fna) + * - `meta`: Groovy Record containing sample information + * - `fna`: Assembled contigs in FASTA format + * + * @output sample_outputs + * - `tsv`: Tab-delimited Stx operon typing results + * + * @output run_outputs + * - `csv`: A merged TSV file with stxtyper results from all samples + */ +nextflow.enable.types = true + +include { STXTYPER as STXTYPER_MODULE } from '../../modules/stxtyper/main' +include { CSVTK_CONCAT } from '../../modules/csvtk/concat/main' +include { gatherCsvtk } from 'plugin/nf-bactopia' + +workflow STXTYPER { + take: + fna: Channel + + main: + ch_stxtyper = STXTYPER_MODULE(fna) + ch_csvtk_concat = CSVTK_CONCAT(gatherCsvtk(ch_stxtyper, 'tsv', [name: 'stxtyper']), 'tsv', 'tsv') + + emit: + // Published outputs + sample_outputs = ch_stxtyper + run_outputs = ch_csvtk_concat +} diff --git a/subworkflows/stxtyper/tests/.nftignore b/subworkflows/stxtyper/tests/.nftignore new file mode 100644 index 000000000..7b276dee3 --- /dev/null +++ b/subworkflows/stxtyper/tests/.nftignore @@ -0,0 +1,2 @@ +**/*.{err,log,stderr,stdout} +**/*.command.* diff --git a/subworkflows/stxtyper/tests/main.nf.test b/subworkflows/stxtyper/tests/main.nf.test new file mode 100644 index 000000000..cfec066a4 --- /dev/null +++ b/subworkflows/stxtyper/tests/main.nf.test @@ -0,0 +1,45 @@ +nextflow_workflow { + name "Test STXTYPER Subworkflow" + script "../main.nf" + workflow "STXTYPER" + tag "subworkflows" + tag "stxtyper" + + test("stxtyper - subworkflow - GCF_001695515") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_001695515"], + fna: file("${params.test_data_dir}/species/escherichia_coli/compressed/GCF_001695515/main/assembler/GCF_001695515.fna.gz") + ) + ) + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def run = workflow.out.run_outputs[0] + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs != null }, + { assert workflow.out.run_outputs != null }, + { assert snapshot( + sample.meta, + sample.tsv, + sample.versions, + run.meta, + run.versions + ).match() }, + { assert sample.results != null }, + { assert run.csv != null }, + { assert run.results != null } + ) + } + } +} diff --git a/subworkflows/stxtyper/tests/main.nf.test.snap b/subworkflows/stxtyper/tests/main.nf.test.snap new file mode 100644 index 000000000..1406ca6b6 --- /dev/null +++ b/subworkflows/stxtyper/tests/main.nf.test.snap @@ -0,0 +1,34 @@ +{ + "stxtyper - subworkflow - GCF_001695515": { + "content": [ + { + "id": "GCF_001695515-STXTYPER:STXTYPER_MODULE", + "logs_dir": "GCF_001695515/tools/stxtyper//logs/", + "name": "GCF_001695515", + "output_dir": "GCF_001695515/tools/stxtyper/", + "process_name": "stxtyper", + "scope": "sample" + }, + "GCF_001695515.tsv:md5,001feff7db6e3fad984fdc36327122cc", + [ + "versions.yml:md5,32d442d87815f24b2b14886add947195" + ], + { + "id": "stxtyper-STXTYPER:CSVTK_CONCAT", + "logs_dir": "merged-results/logs/stxtyper-concat/", + "name": "stxtyper", + "output_dir": "merged-results", + "process_name": "stxtyper-concat", + "scope": "run" + }, + [ + "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c" + ] + ], + "timestamp": "2026-05-21T13:55:41.392691647", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/stxtyper/tests/nextflow.config b/subworkflows/stxtyper/tests/nextflow.config new file mode 100644 index 000000000..3746210c0 --- /dev/null +++ b/subworkflows/stxtyper/tests/nextflow.config @@ -0,0 +1,40 @@ +// Minimal config for subworkflow-level testing of STXTYPER +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "stxtyper" + logo_name = "bactopia-tools" + description = "Identify and type Stx operons from assembled genomic sequences" + ext = "fna" + } + bactopia_version = '4.0.1' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Load module configs for processes in this subworkflow +includeConfig "../../../modules/stxtyper/module.config" +includeConfig "../../../modules/csvtk/concat/module.config" + +// Base config (container resolution + resource labels) +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" + +// Plugin +plugins { + id 'nf-bactopia@2.1.5' +} diff --git a/subworkflows/stxtyper/tests/nf-test.config b/subworkflows/stxtyper/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/subworkflows/stxtyper/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/workflows/bactopia-tools/stxtyper/main.nf b/workflows/bactopia-tools/stxtyper/main.nf new file mode 100644 index 000000000..4d6e2b831 --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/main.nf @@ -0,0 +1,78 @@ +#!/usr/bin/env nextflow +/** + * Identify and type Stx operons from assembled genomic sequences + * + * This Bactopia Tool uses [StxTyper](https://github.com/ncbi/stxtyper) to identify and type stx operons from assembled genomic sequences. + * + * @status stable + * @keywords stx, shiga toxin, typing, stec, virulence, bactopia-tool + * @tags complexity:simple input-type:parameter output-type:multiple features:bactopia-tool,aggregation + * @citation csvtk, stxtyper + * + * @subworkflows utils_bactopia-tools, stxtyper + * + * @input rundir + * Directory containing results from a completed Bactopia analysis run + * + * @section Per-Sample Results + * @publish *.tsv Tab-delimited Stx operon typing results + * + * @section Merged Results + * @publish stxtyper.tsv Merged TSV file containing stxtyper results from all samples + * + * @section Execution Logs + * @publish logs/stxtyper/* Tool execution logs (stdout/stderr) + * @publish logs/nf-* Nextflow execution scripts and logs for debugging + * + * @section Versions + * @publish versions.yml Software version information + */ +nextflow.enable.types = true + +params { + rundir : String +} + +include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' +include { STXTYPER } from '../../../subworkflows/stxtyper/main' +include { collectNextflowLogs } from 'plugin/nf-bactopia' + +workflow { + main: + ch_bactopiatool = BACTOPIATOOL_INIT() + ch_stxtyper = STXTYPER(ch_bactopiatool.assembly) + + publish: + // Per-sample + sample_outputs = ch_stxtyper.sample_outputs + sample_nf_logs = collectNextflowLogs(ch_stxtyper.sample_outputs) + // Run-level + run_outputs = ch_stxtyper.run_outputs + run_nf_logs = collectNextflowLogs(ch_stxtyper.run_outputs) +} + +output { + // Sample-level outputs (stored in ${params.outdir}//) + sample_outputs { + path { r -> + r.results.flatten() >> "${r.meta.output_dir}/" + r.logs.flatten() >> "${r.meta.logs_dir}/" + r.versions.flatten() >> "${r.meta.logs_dir}/" + } + } + sample_nf_logs { + path { meta, f -> f >> "${meta.logs_dir}/nf${f.name}" } + } + + // Run-level outputs (stored in ${params.outdir}/bactopia-runs//) + run_outputs { + path { r -> + r.results.flatten() >> "${params.rundir}/${r.meta.output_dir}/" + r.logs.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + r.versions.flatten() >> "${params.rundir}/${r.meta.logs_dir}/" + } + } + run_nf_logs { + path { meta, f -> f >> "${params.rundir}/${meta.logs_dir}/nf${f.name}" } + } +} diff --git a/workflows/bactopia-tools/stxtyper/nextflow.config b/workflows/bactopia-tools/stxtyper/nextflow.config new file mode 100644 index 000000000..41fe903fe --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/nextflow.config @@ -0,0 +1,91 @@ +// main script name +manifest { + author = 'Robert A. Petit III' + name = 'bactopia' + homePage = 'https://github.com/bactopia/bactopia' + description = 'An extensive workflow for processing sequencing of bacterial genomes.' + mainScript = 'main.nf' + version = '4.0.1' + nextflowVersion = '>=26.04.0' +} + +params { + workflow { + name = "stxtyper" + logo_name = "bactopia-tools" + description = "Identify and type Stx operons from assembled genomic sequences" + ext = ['fna'] + } +} + +// Version +params.bactopia_version = '4.0.1' +manifest.version = "${params.bactopia_version}" + +// Includes +params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +includeConfig "../../../conf/params.config" +includeConfig "../../../conf/params/bactopia-tools.config" + +// Module specific config +includeConfig "../../../modules/csvtk/concat/module.config" +includeConfig "../../../modules/stxtyper/module.config" + +// Set output directory +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode +workflow.output.overwrite = params.force + +// Set up run directory +params.singularity_cache = env("NXF_SINGULARITY_CACHEDIR") ? "${env('NXF_SINGULARITY_CACHEDIR')}" : "${params.singularity_cache}" +params.run_timestamp = new java.util.Date().format('yyyyMMdd-HHmmss') +params.rundir = params.is_ci ? "bactopia-runs/${params.run_name}" : "bactopia-runs/${params.run_name}-${params.run_timestamp}" +params.infodir = "${params.outdir}/${params.rundir}/nf-reports" + +// Load nf-core custom profiles from different Institutions +includeConfig !env('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + +// Load Bactopia custom profiles from different institutions. +// Uncomment in the event a bactopia specific profile is added +//includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bactopia.config" : "/dev/null" + +// Base Config +includeConfig "../../../conf/base.config" + +// Profiles +includeConfig "../../../conf/profiles.config" + +// Reporting configuration +timeline { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-timeline.html" +} + +report { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-report.html" +} + +trace { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-trace.txt" + fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem' +} + +dag { + enabled = true + overwrite = true + file = "${params.infodir}/${params.wf}-dag.svg" +} + +// Plugins +plugins { + id 'nf-bactopia@2.1.5' +} + +bactopia { + parametersSchema = "${projectDir}/nextflow_schema.json" +} \ No newline at end of file diff --git a/workflows/bactopia-tools/stxtyper/nextflow_schema.json b/workflows/bactopia-tools/stxtyper/nextflow_schema.json new file mode 100644 index 000000000..47a1f3c4b --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/nextflow_schema.json @@ -0,0 +1,429 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/bactopia-tools.json", + "title": "stxtyper", + "description": "Identify and type Stx operons from assembled genomic sequences", + "type": "object", + "$defs": { + "input_parameters": { + "title": "Required Parameters", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "help_text": "", + "properties": { + "bactopia": { + "type": "string", + "description": "The path to bactopia results to use as inputs", + "help": "The required inputs will be automatically selected by the subworkflow.", + "fa_icon": "fas fa-bacterium", + "header": "Bactopia Results" + } + } + }, + "filter_parameters": { + "title": "Filtering Parameters", + "type": "object", + "description": "Use these parameters to specify which samples to include or exclude.", + "default": "", + "fa_icon": "fa-solid fa-filter", + "properties": { + "include": { + "type": "string", + "description": "A text file containing sample names (one per line) to include from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-plus" + }, + "exclude": { + "type": "string", + "description": "A text file containing sample names (one per line) to exclude from the analysis", + "help": "The expected format is a single sample per line.", + "fa_icon": "far fa-square-minus" + } + } + }, + "csvtk_concat_parameters": { + "title": "csvtk concat Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "csvtk_concat_opts": { + "type": "string", + "description": "Extra csvtk concat options in quotes", + "help": "", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, + "optional_parameters": { + "title": "Optional Parameters", + "type": "object", + "description": "These optional parameters can be useful in certain settings.", + "default": "", + "fa_icon": "fa-solid fa-gears", + "properties": { + "outdir": { + "type": "string", + "default": "bactopia", + "description": "Base directory to write results to", + "fa_icon": "fas fa-folder" + }, + "skip_compression": { + "type": "boolean", + "default": false, + "description": "Output files will not be compressed", + "help": "Using this parameter can lead to a significant increase in the size of the outputs", + "fa_icon": "fas fa-expand-arrows-alt", + "hidden": true + }, + "datasets": { + "type": "string", + "fa_icon": "fas fa-folder", + "description": "The path to cache datasets to", + "hidden": true + }, + "keep_all_files": { + "type": "boolean", + "default": false, + "description": "Keeps all analysis files created", + "help": "By default, intermediate files are removed. This will not affect the ability to resume Nextflow runs, and only occurs at the end of the process.", + "fa_icon": "fas fa-trash-restore", + "hidden": true + } + } + }, + "max_job_request_parameters": { + "title": "Max Job Request Parameters", + "type": "object", + "fa_icon": "fa-solid fa-arrow-up-right-dots", + "description": "Set the top limit for requested resources for any single job.", + "hidden": true, + "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", + "properties": { + "max_retry": { + "type": "integer", + "description": "Maximum times to retry a process before allowing it to fail.", + "default": 3, + "fa_icon": "fas fa-redo", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of retry attempts for each process. Should be an integer e.g. `--max_retry 1`" + }, + "max_cpus": { + "type": "integer", + "description": "Maximum number of CPUs that can be requested for any single job.", + "default": 4, + "fa_icon": "fas fa-microchip", + "hidden": true, + "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" + }, + "max_memory": { + "type": "string", + "description": "Maximum amount of memory that can be requested for any single job.", + "default": "128.GB", + "fa_icon": "fas fa-memory", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "hidden": true, + "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" + }, + "max_time": { + "type": "string", + "description": "Maximum amount of time that can be requested for any single job.", + "default": "240.h", + "fa_icon": "far fa-clock", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", + "hidden": true, + "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '1.h'`" + }, + "max_downloads": { + "type": "integer", + "description": "Maximum number of samples to download at a time", + "default": 3, + "fa_icon": "fas fa-angle-double-up", + "hidden": true, + "help_text": "Use to set an upper-limit for the number of downloads at a time" + } + } + }, + "nextflow_parameters": { + "title": "Nextflow Configuration Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-solid fa-screwdriver-wrench", + "properties": { + "nfconfig": { + "type": "string", + "description": "A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.", + "help": "This allows you to create profiles specific to your environment (e.g. SGE, AWS, SLURM, etc...).", + "fa_icon": "fas fa-cog", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "hidden": true, + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ] + }, + "infodir": { + "type": "string", + "description": "Directory to keep pipeline Nextflow logs and reports.", + "default": "${params.outdir}/pipeline_info", + "fa_icon": "fas fa-cogs", + "hidden": true + }, + "force": { + "type": "boolean", + "default": false, + "description": "Nextflow will overwrite existing output files.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "cleanup_workdir": { + "type": "boolean", + "default": false, + "description": "After Bactopia is successfully executed, the `work` directory will be deleted.", + "help": "Warning: by doing this you lose the ability to resume workflows.", + "fa_icon": "fas fa-trash-alt", + "hidden": true + } + } + }, + "institutional_config_options": { + "title": "Institutional config options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralized config profiles. These should not be edited.", + "help_text": "The centralized nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "properties": { + "custom_config_version": { + "type": "string", + "description": "Git commit id for Institutional configs.", + "default": "master", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "custom_config_base": { + "type": "string", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", + "hidden": true, + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" + }, + "config_profile_name": { + "type": "string", + "description": "Institutional config name.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_description": { + "type": "string", + "description": "Institutional config description.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_url": { + "type": "string", + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + } + } + }, + "nextflow_profile_parameters": { + "title": "Nextflow Profile Parameters", + "type": "object", + "description": "Parameters to fine-tune your Nextflow setup.", + "default": "", + "hidden": true, + "fa_icon": "fa-regular fa-address-card", + "properties": { + "condadir": { + "type": "string", + "description": "Directory to Nextflow should use for Conda environments", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "registry": { + "type": "string", + "default": "quay.io", + "hidden": true, + "description": "Registry to pull Docker containers from.", + "fa_icon": "fas fa-box" + }, + "datasets_cache": { + "type": "string", + "default": "/.bactopia/datasets", + "description": "Directory where downloaded datasets should be stored.", + "help": "", + "fa_icon": "fas fa-folder" + }, + "singularity_cache": { + "type": "string", + "description": "Directory where remote Singularity images are stored.", + "help": "If using a cluster, it must be accessible from all compute nodes. The NXF_SINGULARITY_CACHEDIR environment variable overrides this parameter", + "fa_icon": "fas fa-folder", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.", + "hidden": true, + "fa_icon": "fas fa-toolbox", + "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues." + }, + "force_rebuild": { + "type": "boolean", + "default": false, + "description": "Force overwrite of existing pre-built environments.", + "fa_icon": "fas fa-recycle", + "hidden": true + }, + "queue": { + "type": "string", + "default": "general,high-memory", + "description": "Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "cluster_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "container_opts": { + "type": "string", + "default": "", + "description": "Additional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D `pwd`'", + "fa_icon": "fas fa-clipboard-list", + "hidden": true + }, + "disable_scratch": { + "type": "boolean", + "default": false, + "description": "All intermediate files created on worker nodes of will be transferred to the head node.", + "help": "Typically with clusters intermediate results are written to a 'scratch' space and only published result files are transferred back", + "fa_icon": "fas fa-toggle-off", + "hidden": true + } + } + }, + "generic_parameters": { + "title": "Helpful Parameters", + "type": "object", + "fa_icon": "fa-solid fa-reply-all", + "description": "Uncommonly used parameters that might be useful.", + "properties": { + "monochrome_logs": { + "type": "boolean", + "description": "Do not use coloured log outputs.", + "fa_icon": "fas fa-palette", + "hidden": true, + "help_text": "Set to disable colourful command line output and live life in monochrome." + }, + "nfdir": { + "type": "boolean", + "description": "Print directory Nextflow has pulled Bactopia to", + "fa_icon": "fas fa-remove-format", + "hidden": true + }, + "sleep_time": { + "type": "integer", + "description": "The amount of time (seconds) Nextflow will wait after setting up datasets before execution.", + "default": 5, + "fa_icon": "far fa-clock", + "hidden": true + }, + "validate_params": { + "type": "boolean", + "default": true, + "fa_icon": "fas fa-tasks", + "description": "Boolean whether to validate parameters against the schema at runtime", + "hidden": true + }, + "help": { + "type": "boolean", + "description": "Display help text.", + "hidden": true, + "fa_icon": "fas fa-question-circle" + }, + "wf": { + "type": "string", + "description": "Specify which workflow or Bactopia Tool to execute", + "default": "bactopia", + "fa_icon": "fas fa-bacteria" + }, + "list_wfs": { + "type": "boolean", + "description": "List the available workflows and Bactopia Tools to use with '--wf'", + "fa_icon": "fas fa-list" + }, + "show_hidden_params": { + "type": "boolean", + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters.", + "description": "Show all params when using `--help`", + "fa_icon": "far fa-eye", + "hidden": true + }, + "help_all": { + "type": "boolean", + "description": "An alias for --help --show_hidden_params", + "fa_icon": "fas fa-question-circle" + }, + "version": { + "type": "boolean", + "description": "Display version text.", + "fa_icon": "fas fa-info" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_parameters" + }, + { + "$ref": "#/$defs/filter_parameters" + }, + { + "$ref": "#/$defs/csvtk_concat_parameters" + }, + { + "$ref": "#/$defs/optional_parameters" + }, + { + "$ref": "#/$defs/max_job_request_parameters" + }, + { + "$ref": "#/$defs/nextflow_parameters" + }, + { + "$ref": "#/$defs/nextflow_profile_parameters" + }, + { + "$ref": "#/$defs/generic_parameters" + } + ] +} \ No newline at end of file diff --git a/workflows/bactopia-tools/stxtyper/tests/.nftignore b/workflows/bactopia-tools/stxtyper/tests/.nftignore new file mode 100644 index 000000000..72a5fcb38 --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/tests/.nftignore @@ -0,0 +1,3 @@ +**/*.{err,gz,html,log,pdf,stderr,stdout} +**/nf.command.* +bactopia-runs/**/nf-reports/*.{dot,html} diff --git a/workflows/bactopia-tools/stxtyper/tests/main.nf.test b/workflows/bactopia-tools/stxtyper/tests/main.nf.test new file mode 100644 index 000000000..1251e9e2f --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_pipeline { + name "Test stxtyper Workflow" + script "../main.nf" + config "../../../../conf/test.config" + tag "workflows" + tag "bactopia-tools" + tag "stxtyper" + + test("stxtyper - GCF_001695515|escherichia_coli|compressed_fasta") { + when { + params { + bactopia_test = "/species/escherichia_coli/compressed" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap new file mode 100644 index 000000000..dcd0ab339 --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap @@ -0,0 +1,51 @@ +{ + "stxtyper - GCF_001695515|escherichia_coli|compressed_fasta": { + "content": [ + 2, + [ + "GCF_001695515", + "GCF_001695515/tools", + "GCF_001695515/tools/stxtyper", + "GCF_001695515/tools/stxtyper/GCF_001695515.tsv", + "GCF_001695515/tools/stxtyper/logs", + "GCF_001695515/tools/stxtyper/logs/nf.command.begin", + "GCF_001695515/tools/stxtyper/logs/nf.command.err", + "GCF_001695515/tools/stxtyper/logs/nf.command.log", + "GCF_001695515/tools/stxtyper/logs/nf.command.out", + "GCF_001695515/tools/stxtyper/logs/nf.command.run", + "GCF_001695515/tools/stxtyper/logs/nf.command.sh", + "GCF_001695515/tools/stxtyper/logs/nf.command.trace", + "GCF_001695515/tools/stxtyper/logs/versions.yml", + "bactopia-runs", + "bactopia-runs/stxtyper", + "bactopia-runs/stxtyper/merged-results", + "bactopia-runs/stxtyper/merged-results/logs", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.begin", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.err", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.log", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.out", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.run", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.sh", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/nf.command.trace", + "bactopia-runs/stxtyper/merged-results/logs/stxtyper-concat/versions.yml", + "bactopia-runs/stxtyper/merged-results/stxtyper.tsv", + "bactopia-runs/stxtyper/nf-reports", + "bactopia-runs/stxtyper/nf-reports/stxtyper-dag.dot", + "bactopia-runs/stxtyper/nf-reports/stxtyper-report.html", + "bactopia-runs/stxtyper/nf-reports/stxtyper-timeline.html" + ], + [ + "GCF_001695515.tsv:md5,001feff7db6e3fad984fdc36327122cc", + "versions.yml:md5,32d442d87815f24b2b14886add947195", + "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c", + "stxtyper.tsv:md5,99f9ffe60fe519d684ee7943641022d2" + ] + ], + "timestamp": "2026-05-21T13:59:39.436267755", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/workflows/bactopia-tools/stxtyper/tests/nf-test.config b/workflows/bactopia-tools/stxtyper/tests/nf-test.config new file mode 100644 index 000000000..8f297479d --- /dev/null +++ b/workflows/bactopia-tools/stxtyper/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "../nextflow.config" + profile "" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} From d7173498fbb5d0b7431a725c9d67b931ab19723c Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 13:40:45 -0600 Subject: [PATCH 19/43] add genome-dl for downloading ncbi dataset genomes --- .vscode/settings.json | 1 + CHANGELOG.md | 14 + catalog.json | 113 ++++++- data/citations.yml | 7 + llms.txt | 2 +- modules/genomedl/main.nf | 137 +++++++++ modules/genomedl/module.config | 49 +++ modules/genomedl/schema.json | 75 +++++ modules/genomedl/tests/main.nf.test | 110 +++++++ modules/genomedl/tests/main.nf.test.snap | 71 +++++ modules/genomedl/tests/nextflow.config | 36 +++ modules/genomedl/tests/nf-test.config | 11 + modules/prokka/module.config | 2 +- modules/prokka/schema.json | 2 +- nextflow.config | 1 + nextflow_schema.json | 27 +- subworkflows/genomedl/main.nf | 75 +++++ subworkflows/genomedl/tests/.nftignore | 2 + subworkflows/genomedl/tests/main.nf.test | 131 ++++++++ subworkflows/genomedl/tests/main.nf.test.snap | 71 +++++ subworkflows/genomedl/tests/nextflow.config | 39 +++ subworkflows/genomedl/tests/nf-test.config | 11 + workflows/bactopia-tools/fastani/main.nf | 16 +- .../bactopia-tools/fastani/nextflow.config | 2 +- .../fastani/nextflow_schema.json | 28 +- .../fastani/tests/main.nf.test.snap | 24 +- workflows/bactopia-tools/mashtree/main.nf | 16 +- .../bactopia-tools/mashtree/nextflow.config | 2 +- .../mashtree/nextflow_schema.json | 28 +- .../mashtree/tests/main.nf.test | 37 +++ .../mashtree/tests/main.nf.test.snap | 33 ++ workflows/bactopia-tools/pangenome/main.nf | 18 +- .../bactopia-tools/pangenome/nextflow.config | 2 +- .../pangenome/nextflow_schema.json | 31 +- .../pangenome/tests/main.nf.test | 40 +++ .../pangenome/tests/main.nf.test.snap | 83 +++++ .../prokka/nextflow_schema.json | 1 + workflows/bactopia-tools/snippy/main.nf | 10 +- .../bactopia-tools/snippy/nextflow.config | 2 +- .../snippy/nextflow_schema.json | 28 +- .../bactopia-tools/snippy/tests/main.nf.test | 50 +++ .../snippy/tests/main.nf.test.snap | 289 ++++++++++++++++++ workflows/staphopia/nextflow_schema.json | 2 +- 43 files changed, 1612 insertions(+), 117 deletions(-) create mode 100644 modules/genomedl/main.nf create mode 100644 modules/genomedl/module.config create mode 100644 modules/genomedl/schema.json create mode 100644 modules/genomedl/tests/main.nf.test create mode 100644 modules/genomedl/tests/main.nf.test.snap create mode 100644 modules/genomedl/tests/nextflow.config create mode 100644 modules/genomedl/tests/nf-test.config create mode 100644 subworkflows/genomedl/main.nf create mode 100644 subworkflows/genomedl/tests/.nftignore create mode 100644 subworkflows/genomedl/tests/main.nf.test create mode 100644 subworkflows/genomedl/tests/main.nf.test.snap create mode 100644 subworkflows/genomedl/tests/nextflow.config create mode 100644 subworkflows/genomedl/tests/nf-test.config diff --git a/.vscode/settings.json b/.vscode/settings.json index 69f4e8d57..e9adda44a 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -315,6 +315,7 @@ "genegaps", "genepred", "Genom", + "genomedl", "genomesize", "genotyphi", "genotyping", diff --git a/CHANGELOG.md b/CHANGELOG.md index 44531250f..b99475e4d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,12 +17,26 @@ sidebar_position: 5000 - Deacon as the default host read scrubber (replaces nohuman as default) - Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules - Three-way scrubber selection: deacon (default), nohuman (`--use_nohuman`), SRA Human Scrubber (`--use_srascrubber`) +- `genomedl` module and subworkflow - download genome assemblies from NCBI Datasets with `genome-dl` + - resolves version-less accessions to the latest assembly version + - subsamples `--species` downloads with `--limit` instead of `shuf | head` + - `--limit` defaults to 100 to prevent accidentally downloading 50k+ genomes (`--limit 0` for no limit) + - subworkflow emits `assemblies` from the named `fna` field, and `reference` from `gbff` when + `--format genbank` is used (Snippy needs an annotated reference), otherwise `fna` - Bump internal bactopia-* pipeline tool versions - `bactopia-gather`: 1.0.5 -> 1.0.6 ### `Changed` - Updated bactopia-teton meta-package from 1.1.3 to 1.1.4 (includes deacon) +- `fastani`, `mashtree`, `pangenome` and `snippy` Bactopia Tools now download genomes with + `genomedl` instead of `ncbigenomedownload` + - `--kingdom` and `--keep_downloads` are no longer available to these tools + - `--limit` now defaults to 100 for `--species` (previously unlimited) + - downloaded genomes are named by accession (`GCF_020736045.1`) rather than by NCBI's full + assembly filename (`GCF_020736045.1_ASM2073604v1_genomic`), which changes output paths and + tree/matrix labels + - `snippy --accession` requires `--format genbank`, since Snippy needs an annotated reference - Deacon modules now use bactopia-teton container instead of standalone deacon container - Teton and scrubber workflows default to deacon instead of nohuman for host read removal - cleanyerreads workflow supports `--use_deacon` flag for host read removal diff --git a/catalog.json b/catalog.json index bcce89d59..29e74293d 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-05-21T19:57:48Z", + "generated": "2026-07-27T18:54:11Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.2.0", "nf_bactopia_version": "2.1.6", @@ -1225,6 +1225,62 @@ ] } }, + "genomedl": { + "description": "Download genome assemblies and annotation files from NCBI Datasets.", + "path": "modules/genomedl/", + "scope": "run", + "process_name": "genomedl", + "tool": { + "name": "genome-dl", + "version": "1.0.0" + }, + "emits": [ + "fna", + "gbff", + "wgs_gbk", + "gff", + "gtf", + "faa", + "gpff", + "cds", + "translated_cds", + "rna", + "features", + "report", + "stats", + "metadata", + "summary", + "json" + ], + "emits_optional": [ + "fna", + "gbff", + "wgs_gbk", + "gff", + "gtf", + "faa", + "gpff", + "cds", + "translated_cds", + "rna", + "features", + "report", + "stats", + "metadata", + "summary", + "json" + ], + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "internet-access", + "resource-download", + "conditional-logic" + ] + } + }, "genotyphi_parse": { "description": "Parse Mykrobe results to genotype *Salmonella* Typhi.", "path": "modules/genotyphi/parse/", @@ -4157,6 +4213,53 @@ ] } }, + "genomedl": { + "description": "Download genome assemblies from NCBI Datasets.", + "path": "subworkflows/genomedl/", + "takes_params": [ + "accessions" + ], + "emits": { + "sample_outputs": [ + "fna", + "gbff", + "wgs_gbk", + "gff", + "gtf", + "faa", + "gpff", + "cds", + "translated_cds", + "rna", + "features", + "report", + "stats", + "metadata", + "summary", + "json" + ], + "run_outputs": [], + "assemblies": [ + "fna" + ], + "reference": [] + }, + "scope": "sample", + "calls": { + "modules": [ + "genomedl" + ] + }, + "tags": { + "complexity": "moderate", + "input_type": "single", + "output_type": "multiple", + "features": [ + "resource-download", + "internet-access" + ] + } + }, "genotyphi": { "description": "Assign genotypes to Salmonella Typhi genomes.", "path": "subworkflows/genotyphi/", @@ -6733,7 +6836,7 @@ ], "subworkflows": [ "fastani", - "ncbigenomedownload" + "genomedl" ] }, "gamma": { @@ -6877,7 +6980,7 @@ ], "subworkflows": [ "mashtree", - "ncbigenomedownload" + "genomedl" ] }, "mcroni": { @@ -6978,7 +7081,7 @@ "gff" ], "subworkflows": [ - "ncbigenomedownload", + "genomedl", "prokka", "pangenome", "clonalframeml", @@ -7175,7 +7278,7 @@ "se" ], "subworkflows": [ - "ncbigenomedownload", + "genomedl", "snippy_run", "snippy_core", "gubbins", diff --git a/data/citations.yml b/data/citations.yml index 3d949dc15..1c0df9838 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -428,6 +428,13 @@ tools: cite: | Stanton RA, Vlachos N, Halpin AL [GAMMA: a tool for the rapid identification, classification, and annotation of translated gene matches from sequencing data.](https://doi.org/10.1093/bioinformatics/btab607) _Bioinformatics_ (2021) + genome_dl: + name: genome-dl + link: https://github.com/rpetit3/genome-dl + description: Download genome assemblies from NCBI Datasets. + cite: | + Petit III RA [genome-dl: Download genomes from NCBI Datasets](https://github.com/rpetit3/genome-dl) (GitHub) + genotyphi: name: GenoTyphi link: https://github.com/katholt/genotyphi diff --git a/llms.txt b/llms.txt index be1811c88..55cefec6f 100644 --- a/llms.txt +++ b/llms.txt @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -105 tool-specific modules live under `modules/`. Each module directory contains: +106 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/genomedl/main.nf b/modules/genomedl/main.nf new file mode 100644 index 000000000..d2e70b1e5 --- /dev/null +++ b/modules/genomedl/main.nf @@ -0,0 +1,137 @@ +/** + * Download genome assemblies and annotation files from NCBI Datasets. + * + * Uses [genome-dl](https://github.com/rpetit3/genome-dl) to query the NCBI Datasets v2 REST API + * for assembly metadata, then download the requested file formats directly from the NCBI FTP + * site. Accessions are resolved to their latest version before download, and species queries + * are subsampled to the first `--limit` assemblies in NCBI relevance order (reference first). + * + * @status stable + * @keywords ncbi, datasets, download, genome, assembly, fasta, utility + * @tags complexity:moderate input-type:single output-type:multiple features:internet-access,resource-download,conditional-logic + * @citation genome_dl + * + * @note Internet Required + * Queries the NCBI Datasets v2 REST API and downloads from the NCBI FTP site. Setting the + * `NCBI_API_KEY` environment variable raises the API rate limit from 5 to 10 requests per second. + * + * @note Species Downloads Are Capped + * `--limit` defaults to 100 so a broad `--species` cannot accidentally pull the tens of + * thousands of assemblies NCBI holds for common taxa. Raise it, or use `--limit 0` for no + * limit, only when that is genuinely intended. + * + * @input accessions? + * A path to a text file containing a list of NCBI Assembly accessions (one per line) + * + * @output record(meta, fna?, gbff?, wgs_gbk?, gff?, gtf?, faa?, gpff?, cds?, translated_cds?, rna?, features?, report?, stats?, metadata?, summary?, json?, results, logs, nf_logs, versions) + * - `fna?`: FASTA format of the genomic nucleotide sequence(s) (*.fna.gz) + * - `gbff?`: GenBank format of the genomic sequence(s) (*.gbff.gz) + * - `wgs_gbk?`: GenBank flat file format of the WGS master (*.wgsmaster.gbff.gz) + * - `gff?`: Annotation of the genomic sequence(s) in GFF3 format (*.gff.gz) + * - `gtf?`: Annotation of the genomic sequence(s) in GTF format (*.gtf.gz) + * - `faa?`: FASTA format of the accessioned protein products (*.faa.gz) + * - `gpff?`: GenPept format of the accessioned protein products (*.gpff.gz) + * - `cds?`: FASTA format of the nucleotide sequences corresponding to all CDS features + * - `translated_cds?`: FASTA format of the protein sequences corresponding to all CDS features + * - `rna?`: FASTA format of the nucleotide sequences corresponding to all RNA features + * - `features?`: Tab-delimited text file reporting locations and attributes for a subset of features + * - `report?`: Tab-delimited text file reporting assembly unit names, roles, and relationships + * - `stats?`: Tab-delimited text file reporting assembly statistics + * - `metadata?`: Tab-delimited NCBI Datasets metadata for each downloaded assembly + * - `summary?`: Human-readable run summary of the version, parameters, and results + * - `json?`: Machine-readable run report of the parameters, results, and per-assembly metadata + */ +nextflow.enable.types = true + +// bactopia-lint: ignore M017,M026 +process GENOMEDL { + label 'process_low' + + conda "${task.ext.condaDir}/${task.ext.toolName}" + container "${task.ext.container}" + + input: + accessions : Path? + + stage: + stageAs accessions, 'staging/accessions/*' + + output: + record( + // Named fields (used downstream) + meta: meta, + // Use the [0-9] to separate a genomic FASTA from the cds.fna.gz/rna.fna.gz variants + fna: files("*[0-9].fna.gz", optional: true), + gbff: files("*[0-9].gbff.gz", optional: true), + wgs_gbk: files("*.wgsmaster.gbff.gz", optional: true), + gff: files("*.gff.gz", optional: true), + gtf: files("*.gtf.gz", optional: true), + faa: files("*[0-9].faa.gz", optional: true), + gpff: files("*.gpff.gz", optional: true), + cds: files("*.cds.fna.gz", optional: true), + translated_cds: files("*.translated_cds.faa.gz", optional: true), + rna: files("*.rna.fna.gz", optional: true), + features: files("*.feature_table.txt.gz", optional: true), + report: files("*.assembly_report.txt", optional: true), + stats: files("*.assembly_stats.txt", optional: true), + metadata: files("*-metadata.tsv", optional: true), + summary: files("*-summary.txt", optional: true), + json: files("*.json", optional: true), + // Generic fields (used for publishing) + results: [ + files("*.gz", optional: true), + files("*.txt", optional: true), + files("*.tsv", optional: true), + files("*.json", optional: true) + ], + logs: files("*.{log,err}", optional: true), + nf_logs: files(".command.*"), + versions: files("versions.yml") + ) + + script: + prefix = task.ext.prefix ?: task.ext.meta_id + meta = record( + id: task.ext.meta_id, + name: task.ext.meta_id, + limit: task.ext.meta_limit, + accession: task.ext.meta_accession, + species: task.ext.meta_species, + scope: task.ext.scope, + process_name: task.ext.process_name, + output_dir: task.ext.process_name, + logs_dir: "${task.ext.process_name}/logs" + ) + + def has_accession = task.ext.meta_accession != null + def has_accessions = accessions != null + def has_species = task.ext.meta_species != null + def opts = "${task.ext.args} --outdir ./ --cpus ${task.cpus} --max-attempts ${task.ext.max_retry}" + """ + # genome-dl can't mix --accession, --accessions, and --species, so run for each + if [ "${has_accession}" == "true" ]; then + genome-dl ${opts} \\ + --prefix ${prefix}-accession \\ + --accession ${task.ext.meta_accession} + fi + + if [ "${has_accessions}" == "true" ]; then + genome-dl ${opts} \\ + --prefix ${prefix}-accessions \\ + --accessions ${accessions} + fi + + if [ "${has_species}" == "true" ]; then + genome-dl ${opts} ${task.ext.args2} \\ + --prefix ${prefix}-species \\ + --species "${task.ext.meta_species}" + fi + + # Cleanup + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + genomedl: \$(echo \$(genome-dl --version 2>&1) | sed 's/.*version //') + END_VERSIONS + """ +} diff --git a/modules/genomedl/module.config b/modules/genomedl/module.config new file mode 100644 index 000000000..d81651f77 --- /dev/null +++ b/modules/genomedl/module.config @@ -0,0 +1,49 @@ +// bactopia-lint: ignore MC009,JS004 +params { + // genomedl + accession = null + accessions = null + assembly_level = "complete" + format = "fasta" + genomedl_allow_outdated = false + limit = 100 + max_retry = 10 + section = "refseq" + species = null +} + +process { + withName: 'GENOMEDL' { + ext.wf = params.wf + ext.scope = "run" + ext.subdir = "" + ext.logs_subdir = "" + ext.process_name = "genomedl" + + // Tool arguments + ext.args = [ + "--formats ${params.format}", + params.genomedl_allow_outdated ? "--allow-outdated" : "" + ].join(' ').replaceAll("\\s{2,}", " ").trim() + + // Species-only arguments (--section, --assembly-level and --limit only apply to --species) + ext.args2 = [ + "--section ${params.section}", + "--assembly-level ${params.assembly_level}", + "--limit ${params.limit}" + ].join(' ').replaceAll("\\s{2,}", " ").trim() + + // Environment information + ext.toolName = "bioconda::genome-dl=1.0.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/genome-dl:1.0.0--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/genome-dl:1.0.0--pyhdfd78af_0" + ext.condaDir = "${params.condadir}" + + // Module-specific parameters + ext.max_retry = params.max_retry + ext.meta_id = "genomedl" + ext.meta_limit = params.limit + ext.meta_accession = params.accession + ext.meta_species = params.species + } +} diff --git a/modules/genomedl/schema.json b/modules/genomedl/schema.json new file mode 100644 index 000000000..b3f6f8aeb --- /dev/null +++ b/modules/genomedl/schema.json @@ -0,0 +1,75 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/genomedl/schema.json", + "title": "genome-dl Module", + "description": "A module to download genome assemblies from NCBI Datasets", + "type": "object", + "$defs": { + "genomedl_parameters": { + "title": "genome-dl Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "species": { + "type": "string", + "description": "Name of the species to download assemblies", + "fa_icon": "fas fa-font" + }, + "accession": { + "type": "string", + "description": "An NCBI Assembly accession to be downloaded", + "help": "Version-less accessions (e.g. GCF_000005845) are resolved to the latest version.", + "fa_icon": "fas fa-font" + }, + "accessions": { + "type": "string", + "description": "An file of NCBI Assembly accessions (one per line) to be downloaded", + "fa_icon": "fas fa-font" + }, + "format": { + "type": "string", + "default": "fasta", + "description": "Comma separated list of formats to download", + "help": "Choose from fasta, genbank, wgs, gff, gtf, protein, genpept, cds, translated-cds, rna, feature-table, assembly-report, assembly-stats or all.", + "fa_icon": "fas fa-font" + }, + "section": { + "type": "string", + "default": "refseq", + "description": "NCBI section to download", + "help": "Only applies to `--species`. Choose from refseq, genbank or all.", + "fa_icon": "fas fa-font", + "hidden": true + }, + "assembly_level": { + "type": "string", + "default": "complete", + "description": "Comma separated list of assembly levels to download", + "help": "Only applies to `--species`. Choose from complete, chromosome, scaffold, contig or all.", + "fa_icon": "fas fa-font", + "hidden": true + }, + "limit": { + "type": "integer", + "default": 100, + "description": "Limit the number of assemblies to download", + "help": "Only applies to `--species`, limit to first N assemblies returned by NCBI. Use 0 for no limit.", + "fa_icon": "fas fa-sort-numeric-up" + }, + "genomedl_allow_outdated": { + "type": "boolean", + "default": false, + "description": "Download an explicitly requested outdated accession version instead of erroring", + "fa_icon": "fas fa-toggle-on" + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/genomedl_parameters" + } + ] +} diff --git a/modules/genomedl/tests/main.nf.test b/modules/genomedl/tests/main.nf.test new file mode 100644 index 000000000..04854ad40 --- /dev/null +++ b/modules/genomedl/tests/main.nf.test @@ -0,0 +1,110 @@ +nextflow_process { + name "Test GENOMEDL" + script "../main.nf" + process "GENOMEDL" + tag "modules" + tag "genomedl" + + test("genomedl - module - single accession") { + + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + // Portiera aleyrodidarum (~360 kb), version-less to test accession resolution + accession = "GCF_000292685" + format = "fasta" + } + process { + """ + input[0] = null + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.versions + ).match() }, + // GCF_000292685 resolves to GCF_000292685.1, and the genomic FASTA glob must + // not also pick up the *.cds.fna.gz / *.rna.fna.gz variants + { assert record.fna.size() == 1 }, + { assert record.fna[0].toString().endsWith("/GCF_000292685.1.fna.gz") }, + { assert record.metadata.size() == 1 }, + { assert record.summary.size() == 1 }, + { assert record.json.size() == 1 } + ) + } + } + + test("genomedl - module - species with limit") { + + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + // The taxon has 14 complete RefSeq assemblies, --limit trims the download to one + species = "Candidatus Portiera aleyrodidarum" + assembly_level = "complete" + format = "fasta" + limit = 1 + } + process { + """ + input[0] = null + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.versions + ).match() }, + { assert record.fna.size() == 1 }, + { assert record.metadata.size() == 1 }, + { assert record.summary.size() == 1 }, + { assert record.json.size() == 1 } + ) + } + } + + test("genomedl - module - accessions file") { + + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + format = "fasta" + } + process { + """ + input[0] = file("${params.test_data_dir}/datasets/generic/test-assembly-accessions.txt") + """ + } + } + + then { + def record = process.out[0][0] + def published = record.results.flatten().collect { p -> p.toString() } + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.versions + ).match() }, + // Two accessions, one comment line that genome-dl must skip + { assert record.fna.size() == 2 }, + { assert record.metadata.size() == 1 }, + { assert record.summary.size() == 1 }, + { assert record.json.size() == 1 }, + // The staged input list must not be republished as a result + { assert published.every { p -> !p.endsWith("test-assembly-accessions.txt") } } + ) + } + } +} diff --git a/modules/genomedl/tests/main.nf.test.snap b/modules/genomedl/tests/main.nf.test.snap new file mode 100644 index 000000000..21a1d2376 --- /dev/null +++ b/modules/genomedl/tests/main.nf.test.snap @@ -0,0 +1,71 @@ +{ + "genomedl - module - species with limit": { + "content": [ + { + "accession": null, + "id": "genomedl", + "limit": 1, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": "Candidatus Portiera aleyrodidarum" + }, + [ + "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" + ] + ], + "timestamp": "2026-07-27T10:23:32.083383414", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "genomedl - module - single accession": { + "content": [ + { + "accession": "GCF_000292685", + "id": "genomedl", + "limit": 100, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": null + }, + [ + "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" + ] + ], + "timestamp": "2026-07-27T10:23:24.497928112", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "genomedl - module - accessions file": { + "content": [ + { + "accession": null, + "id": "genomedl", + "limit": 100, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": null + }, + [ + "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" + ] + ], + "timestamp": "2026-07-27T10:23:39.277366568", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/genomedl/tests/nextflow.config b/modules/genomedl/tests/nextflow.config new file mode 100644 index 000000000..c8dece7a8 --- /dev/null +++ b/modules/genomedl/tests/nextflow.config @@ -0,0 +1,36 @@ +// Minimal config for module-level testing of GENOMEDL +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "genomedl" + logo_name = "bactopia-tools" + description = "Download genome assemblies from NCBI Datasets" + ext = "fna" + } + + bactopia_version = '4.0.0' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +includeConfig "../module.config" +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" diff --git a/modules/genomedl/tests/nf-test.config b/modules/genomedl/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/modules/genomedl/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/modules/prokka/module.config b/modules/prokka/module.config index 79122eb75..a4efb615f 100644 --- a/modules/prokka/module.config +++ b/modules/prokka/module.config @@ -6,7 +6,7 @@ params { prokka_debug = false prokka_evalue = "1e-09" prokka_opts = "" - prokka_proteins = "${projectDir}/data/proteins.faa" + prokka_proteins = "./data/proteins.faa" } process { diff --git a/modules/prokka/schema.json b/modules/prokka/schema.json index f2657665a..1ec19aa52 100644 --- a/modules/prokka/schema.json +++ b/modules/prokka/schema.json @@ -14,7 +14,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "${projectDir}/data/proteins.faa", + "default": "./data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, diff --git a/nextflow.config b/nextflow.config index 58a772fbd..c034d1db4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -62,6 +62,7 @@ includeConfig "./modules/ssuissero/module.config" includeConfig "./modules/agrvate/module.config" includeConfig "./modules/spatyper/module.config" includeConfig "./modules/sccmec/module.config" +includeConfig "./modules/staphscan/module.config" includeConfig "./modules/stecfinder/module.config" includeConfig "./modules/tbprofiler/profile/module.config" includeConfig "./modules/tbprofiler/collate/module.config" diff --git a/nextflow_schema.json b/nextflow_schema.json index 84fb0c788..ece72f94c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1008,7 +1008,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "${projectDir}/data/proteins.faa", + "default": "./data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font", "hidden": true @@ -1761,6 +1761,28 @@ } } }, + "staphscan_parameters": { + "title": "StaphSCAN Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "staphscan_modules": { + "type": "string", + "default": "", + "description": "Comma-separated list of modules to run", + "fa_icon": "fas fa-font", + "hidden": true + }, + "staphscan_db_mlst": { + "type": "string", + "description": "Path or tarball to custom MLST database", + "fa_icon": "fas fa-font", + "hidden": true + } + } + }, "stecfinder_parameters": { "title": "STECFinder Parameters", "type": "object", @@ -2402,6 +2424,9 @@ { "$ref": "#/$defs/sccmec_parameters" }, + { + "$ref": "#/$defs/staphscan_parameters" + }, { "$ref": "#/$defs/stecfinder_parameters" }, diff --git a/subworkflows/genomedl/main.nf b/subworkflows/genomedl/main.nf new file mode 100644 index 000000000..d949d30f9 --- /dev/null +++ b/subworkflows/genomedl/main.nf @@ -0,0 +1,75 @@ +/** + * Download genome assemblies from NCBI Datasets. + * + * This subworkflow downloads genome assemblies using + * [genome-dl](https://github.com/rpetit3/genome-dl), which resolves accessions to their latest + * version and subsamples species queries before fetching files from the NCBI FTP site. The + * downloaded assemblies are fanned out into per-genome records for downstream analysis, and the + * first assembly is exposed separately for use as a reference genome. + * + * @status stable + * @keywords download, ncbi, datasets, genome, assembly, refseq + * @tags complexity:moderate input-type:single output-type:multiple features:resource-download,internet-access + * @citation genome_dl + * + * @modules genomedl as genomedl_module + * + * @input accessions + * A file containing NCBI Assembly accessions, one per line. May be combined with the `--accession` and `--species` parameters. + * + * @output sample_outputs + * - `fna`: Genomic nucleotide sequences in FASTA format + * - `gbff`: GenBank format genome sequences + * - `wgs_gbk`: WGS master records in GenBank format + * - `gff`: Genome annotations in GFF3 format + * - `gtf`: Genome annotations in GTF format + * - `faa`: Protein sequences in FASTA format + * - `gpff`: Protein sequences in GenPept format + * - `cds`: CDS nucleotide sequences in FASTA format + * - `translated_cds`: CDS protein sequences in FASTA format + * - `rna`: RNA feature nucleotide sequences in FASTA format + * - `features`: Feature table with locations and attributes + * - `report`: Assembly report with unit and sequence relationships + * - `stats`: Assembly statistics + * - `metadata`: NCBI Datasets metadata for each downloaded assembly + * - `summary`: Human-readable run summary of the version, parameters, and results + * - `json`: Machine-readable run report of the parameters, results, and per-assembly metadata + * + * @output run_outputs + * + * @output assemblies + * - `fna`: Individual downloaded assembly in FASTA format + * + * @output reference + * First downloaded genome for use as a reference. Prefers GenBank (`--format genbank`) over + * FASTA, since annotation-aware consumers such as Snippy require a GenBank reference. + */ +nextflow.enable.types = true + +include { GENOMEDL as GENOMEDL_MODULE } from '../../modules/genomedl/main' + +workflow GENOMEDL { + + take: + accessions: Path? + + main: + ch_genomedl = GENOMEDL_MODULE(accessions) + // Fan out on the named `fna` field rather than `results`, which also carries the metadata + // TSV, run summary, and JSON report that genome-dl always writes + ch_assemblies = ch_genomedl.map { r -> r.fna }.flatten().map { path -> + def sample_name = file(path).getSimpleName() + record(meta: record(id: sample_name, name: sample_name), fna: path) + } + // Prefer GenBank over FASTA: consumers of `reference` (Snippy) need the annotations, and + // `--format` decides which of the two genome-dl actually wrote + ch_reference = ch_genomedl.map { r -> r.gbff ? r.gbff : r.fna }.flatten().first() + + emit: + // Downstream inputs + assemblies = ch_assemblies + reference = ch_reference + // Published outputs + sample_outputs = ch_genomedl + run_outputs = channel.empty() +} diff --git a/subworkflows/genomedl/tests/.nftignore b/subworkflows/genomedl/tests/.nftignore new file mode 100644 index 000000000..7b276dee3 --- /dev/null +++ b/subworkflows/genomedl/tests/.nftignore @@ -0,0 +1,2 @@ +**/*.{err,log,stderr,stdout} +**/*.command.* diff --git a/subworkflows/genomedl/tests/main.nf.test b/subworkflows/genomedl/tests/main.nf.test new file mode 100644 index 000000000..372f5ae7c --- /dev/null +++ b/subworkflows/genomedl/tests/main.nf.test @@ -0,0 +1,131 @@ +nextflow_workflow { + name "Test GENOMEDL Subworkflow" + script "../main.nf" + workflow "GENOMEDL" + tag "subworkflows" + tag "genomedl" + + test("genomedl - subworkflow - single accession") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + // Portiera aleyrodidarum (~360 kb), version-less to test accession resolution + accession = "GCF_000292685" + format = "fasta" + } + workflow { + """ + input[0] = null + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def assemblies = workflow.out.assemblies + assertAll( + { assert workflow.success }, + { assert snapshot( + sample.meta, + sample.versions + ).match() }, + // One downloaded genome fans out to one assembly record + { assert assemblies.size() == 1 }, + { assert assemblies[0].meta.name == "GCF_000292685" }, + { assert workflow.out.reference != null } + ) + } + } + + test("genomedl - subworkflow - accessions file") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + format = "fasta" + } + workflow { + """ + input[0] = file("${params.test_data_dir}/datasets/generic/test-assembly-accessions.txt") + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def assemblies = workflow.out.assemblies + def names = assemblies.collect { r -> r.meta.name }.sort() + assertAll( + { assert workflow.success }, + { assert snapshot( + sample.meta, + sample.versions + ).match() }, + // Two accessions in the file fan out to two assembly records + { assert assemblies.size() == 2 }, + { assert names == ["GCF_002849975", "GCF_002849995"] } + ) + } + } + + test("genomedl - subworkflow - species with limit") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + // The taxon has 14 complete RefSeq assemblies, --limit trims the download to two + species = "Candidatus Portiera aleyrodidarum" + assembly_level = "complete" + format = "fasta" + limit = 2 + } + workflow { + """ + input[0] = null + """ + } + } + + then { + def sample = workflow.out.sample_outputs[0] + def assemblies = workflow.out.assemblies + assertAll( + { assert workflow.success }, + { assert snapshot( + sample.meta, + sample.versions + ).match() }, + // NCBI relevance order is not stable, so assert the shape rather than accessions + { assert assemblies.size() == 2 }, + { assert assemblies.every { r -> r.meta.name.startsWith("GCF_") } }, + { assert assemblies.every { r -> r.meta.name == r.meta.id } } + ) + } + } + + test("genomedl - subworkflow - genbank reference") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + accession = "GCF_000292685" + format = "genbank" + } + workflow { + """ + input[0] = null + """ + } + } + + then { + def reference = workflow.out.reference + assertAll( + { assert workflow.success }, + // Snippy needs the annotations, so `reference` must resolve to the GenBank + // download rather than falling back to an empty `fna` field + { assert reference != null }, + { assert file(reference[0]).name.endsWith(".gbff.gz") }, + // `--format genbank` writes no FASTA, so nothing fans out to `assemblies` + { assert workflow.out.assemblies.size() == 0 } + ) + } + } +} diff --git a/subworkflows/genomedl/tests/main.nf.test.snap b/subworkflows/genomedl/tests/main.nf.test.snap new file mode 100644 index 000000000..107d81119 --- /dev/null +++ b/subworkflows/genomedl/tests/main.nf.test.snap @@ -0,0 +1,71 @@ +{ + "genomedl - subworkflow - accessions file": { + "content": [ + { + "accession": null, + "id": "genomedl", + "limit": 100, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": null + }, + [ + "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" + ] + ], + "timestamp": "2026-07-27T10:39:14.382642688", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "genomedl - subworkflow - species with limit": { + "content": [ + { + "accession": null, + "id": "genomedl", + "limit": 2, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": "Candidatus Portiera aleyrodidarum" + }, + [ + "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" + ] + ], + "timestamp": "2026-07-27T10:39:22.848479262", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "genomedl - subworkflow - single accession": { + "content": [ + { + "accession": "GCF_000292685", + "id": "genomedl", + "limit": 100, + "logs_dir": "genomedl/logs", + "name": "genomedl", + "output_dir": "genomedl", + "process_name": "genomedl", + "scope": "run", + "species": null + }, + [ + "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" + ] + ], + "timestamp": "2026-07-27T10:39:06.172839858", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/subworkflows/genomedl/tests/nextflow.config b/subworkflows/genomedl/tests/nextflow.config new file mode 100644 index 000000000..62f503f48 --- /dev/null +++ b/subworkflows/genomedl/tests/nextflow.config @@ -0,0 +1,39 @@ +// Minimal config for subworkflow-level testing of GENOMEDL +nextflow.enable.types = true +nextflow.enable.strict = true + +params { + workflow { + name = "genomedl" + logo_name = "bactopia-tools" + description = "Download genome assemblies from NCBI Datasets" + ext = "fna" + } + bactopia_version = '4.0.0' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + wf = params.workflow.name + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Load module configs for processes in this subworkflow +includeConfig "../../../modules/genomedl/module.config" + +// Base config (container resolution + resource labels) +includeConfig "../../../conf/base.config" +includeConfig "../../../conf/profiles.config" + +// Plugin +plugins { + id 'nf-bactopia@2.1.6' +} diff --git a/subworkflows/genomedl/tests/nf-test.config b/subworkflows/genomedl/tests/nf-test.config new file mode 100644 index 000000000..1f765f697 --- /dev/null +++ b/subworkflows/genomedl/tests/nf-test.config @@ -0,0 +1,11 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "nextflow.config" + profile "docker" + options "--is_ci --max_memory 8.GB" + + plugins { + load "nft-utils@0.0.5" + } +} diff --git a/workflows/bactopia-tools/fastani/main.nf b/workflows/bactopia-tools/fastani/main.nf index 79fc98e63..d44629679 100644 --- a/workflows/bactopia-tools/fastani/main.nf +++ b/workflows/bactopia-tools/fastani/main.nf @@ -4,14 +4,14 @@ * * This Bactopia Tool uses [FastANI](https://github.com/ParBLiSS/FastANI) to calculate the average * nucleotide identity (ANI) between samples. It can also calculate ANI against reference genomes - * by downloading RefSeq assemblies using NCBI genome download. + * by downloading NCBI assemblies using genome-dl. * * @status stable * @keywords ani, average nucleotide identity, similarity, comparative genomics, bactopia-tool * @tags complexity:moderate input-type:parameter output-type:multiple features:bactopia-tool,comparative * @citation fastani * - * @subworkflows utils_bactopia-tools, fastani, ncbigenomedownload + * @subworkflows utils_bactopia-tools, fastani, genomedl * * @input rundir * Directory containing results from a completed Bactopia analysis run @@ -23,13 +23,13 @@ * Perform pairwise ANI calculation between all samples * * @input species - * Species name to download all RefSeq genomes for comparison + * Species name to download all NCBI genomes for comparison * * @input accession - * Specific NCBI Assembly RefSeq accession to download + * Specific NCBI Assembly accession to download * * @input accessions - * Path to file containing list of NCBI accessions to download + * Path to file containing list of NCBI Assembly accessions to download * * @section Per-Sample Results * @publish *.tsv FastANI results of samples against reference @@ -59,7 +59,7 @@ params { include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' include { FASTANI } from '../../../subworkflows/fastani/main' -include { NCBIGENOMEDOWNLOAD } from '../../../subworkflows/ncbigenomedownload/main' +include { GENOMEDL } from '../../../subworkflows/genomedl/main' include { collectNextflowLogs } from 'plugin/nf-bactopia' workflow { @@ -77,8 +77,8 @@ workflow { // Download if applicable if (params.species || params.accession || params.accessions) { - ch_ncbigenomedownload = NCBIGENOMEDOWNLOAD(params.accessions) - ch_reference = ch_reference.mix(ch_ncbigenomedownload.assemblies) + ch_genomedl = GENOMEDL(params.accessions) + ch_reference = ch_reference.mix(ch_genomedl.assemblies) } // Add query if pairwise diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index 982fbddce..2192e7505 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -30,7 +30,7 @@ includeConfig "../../../conf/params/bactopia-tools.config" // Module specific config includeConfig "../../../modules/csvtk/concat/module.config" includeConfig "../../../modules/fastani/module.config" -includeConfig "../../../modules/ncbigenomedownload/module.config" +includeConfig "../../../modules/genomedl/module.config" // Set output directory outputDir = params.outdir diff --git a/workflows/bactopia-tools/fastani/nextflow_schema.json b/workflows/bactopia-tools/fastani/nextflow_schema.json index 4cbf4b735..e51a921a7 100644 --- a/workflows/bactopia-tools/fastani/nextflow_schema.json +++ b/workflows/bactopia-tools/fastani/nextflow_schema.json @@ -98,8 +98,8 @@ } } }, - "ncbigenomedownload_parameters": { - "title": "NCBI Genome Download Parameters", + "genomedl_parameters": { + "title": "genome-dl Parameters", "type": "object", "description": "", "default": "", @@ -113,6 +113,7 @@ "accession": { "type": "string", "description": "An NCBI Assembly accession to be downloaded", + "help": "Version-less accessions (e.g. GCF_000005845) are resolved to the latest version.", "fa_icon": "fas fa-font" }, "accessions": { @@ -124,12 +125,14 @@ "type": "string", "default": "fasta", "description": "Comma separated list of formats to download", + "help": "Choose from fasta, genbank, wgs, gff, gtf, protein, genpept, cds, translated-cds, rna, feature-table, assembly-report, assembly-stats or all.", "fa_icon": "fas fa-font" }, "section": { "type": "string", "default": "refseq", "description": "NCBI section to download", + "help": "Only applies to `--species`. Choose from refseq, genbank or all.", "fa_icon": "fas fa-font", "hidden": true }, @@ -137,26 +140,21 @@ "type": "string", "default": "complete", "description": "Comma separated list of assembly levels to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "kingdom": { - "type": "string", - "default": "bacteria", - "description": "Comma separated list of formats to download", + "help": "Only applies to `--species`. Choose from complete, chromosome, scaffold, contig or all.", "fa_icon": "fas fa-font", "hidden": true }, "limit": { - "type": "string", + "type": "integer", + "default": 100, "description": "Limit the number of assemblies to download", - "help": "If the the number of available genomes exceeds the given limit, a random subset will be selected.", - "fa_icon": "fas fa-font" + "help": "Only applies to `--species`, limit to first N assemblies returned by NCBI. Use 0 for no limit.", + "fa_icon": "fas fa-sort-numeric-up" }, - "keep_downloads": { + "genomedl_allow_outdated": { "type": "boolean", "default": false, - "description": "Save downloaded files into the bactopia-runs folder", + "description": "Download an explicitly requested outdated accession version instead of erroring", "fa_icon": "fas fa-toggle-on" } } @@ -517,7 +515,7 @@ "$ref": "#/$defs/csvtk_concat_parameters" }, { - "$ref": "#/$defs/ncbigenomedownload_parameters" + "$ref": "#/$defs/genomedl_parameters" }, { "$ref": "#/$defs/optional_parameters" diff --git a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap index 9ba27f3de..b448de92a 100644 --- a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap @@ -5,17 +5,17 @@ [ "bactopia-runs", "bactopia-runs/fastani", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/GCF_020736045.1_ASM2073604v1_genomic.tsv", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.begin", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.err", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.log", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.out", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.run", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.sh", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/nf.command.trace", - "bactopia-runs/fastani/GCF_020736045.1_ASM2073604v1_genomic/logs/versions.yml", + "bactopia-runs/fastani/GCF_020736045.1", + "bactopia-runs/fastani/GCF_020736045.1/GCF_020736045.1.tsv", + "bactopia-runs/fastani/GCF_020736045.1/logs", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.begin", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.err", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.log", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.out", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.run", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.sh", + "bactopia-runs/fastani/GCF_020736045.1/logs/nf.command.trace", + "bactopia-runs/fastani/GCF_020736045.1/logs/versions.yml", "bactopia-runs/fastani/merged-results", "bactopia-runs/fastani/merged-results/fastani.tsv", "bactopia-runs/fastani/merged-results/logs", @@ -38,7 +38,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-04-29T11:23:18.750990614", + "timestamp": "2026-07-27T13:08:38.973757707", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashtree/main.nf b/workflows/bactopia-tools/mashtree/main.nf index ed5cf085b..6a49488b9 100644 --- a/workflows/bactopia-tools/mashtree/main.nf +++ b/workflows/bactopia-tools/mashtree/main.nf @@ -4,26 +4,26 @@ * * This Bactopia Tool uses [Mashtree](https://github.com/lskatz/mashtree) to create a phylogenetic tree * of samples using [Mash](https://github.com/marbl/Mash) distances. It can include reference - * genomes from RefSeq by downloading them with NCBI genome download. + * genomes from NCBI by downloading them with genome-dl. * * @status stable * @keywords phylogeny, tree, mash, distance, comparative genomics, bactopia-tool * @tags complexity:moderate input-type:parameter output-type:multiple features:bactopia-tool,phylogeny,comparative * @citation mashtree * - * @subworkflows utils_bactopia-tools, mashtree, ncbigenomedownload + * @subworkflows utils_bactopia-tools, mashtree, genomedl * * @input rundir * Directory containing results from a completed Bactopia analysis run * * @input species - * Species name to download all RefSeq genomes for comparison + * Species name to download all NCBI genomes for comparison * * @input accession - * Specific NCBI Assembly RefSeq accession to download + * Specific NCBI Assembly accession to download * * @input accessions - * Path to file containing list of NCBI accessions to download + * Path to file containing list of NCBI Assembly accessions to download * * @section Phylogenetic Analysis * @publish mashtree.dnd Newick format tree file @@ -52,7 +52,7 @@ params { include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' include { MASHTREE } from '../../../subworkflows/mashtree/main' -include { NCBIGENOMEDOWNLOAD } from '../../../subworkflows/ncbigenomedownload/main' +include { GENOMEDL } from '../../../subworkflows/genomedl/main' include { gather } from 'plugin/nf-bactopia' include { collectNextflowLogs } from 'plugin/nf-bactopia' @@ -63,8 +63,8 @@ workflow { // Download if applicable if (params.species || params.accession || params.accessions) { - ch_ncbigenomedownload = NCBIGENOMEDOWNLOAD(params.accessions) - ch_samples = ch_samples.mix(ch_ncbigenomedownload.assemblies) + ch_genomedl = GENOMEDL(params.accessions) + ch_samples = ch_samples.mix(ch_genomedl.assemblies) } ch_mashtree = MASHTREE(gather(ch_samples, 'fna', [name: 'mashtree'])) diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 151cca771..1ecd73c78 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -29,7 +29,7 @@ includeConfig "../../../conf/params/bactopia-tools.config" // Module specific config includeConfig "../../../modules/mashtree/module.config" -includeConfig "../../../modules/ncbigenomedownload/module.config" +includeConfig "../../../modules/genomedl/module.config" // Set output directory outputDir = params.outdir diff --git a/workflows/bactopia-tools/mashtree/nextflow_schema.json b/workflows/bactopia-tools/mashtree/nextflow_schema.json index a4a24cf8f..e04a494cc 100644 --- a/workflows/bactopia-tools/mashtree/nextflow_schema.json +++ b/workflows/bactopia-tools/mashtree/nextflow_schema.json @@ -101,8 +101,8 @@ } } }, - "ncbigenomedownload_parameters": { - "title": "NCBI Genome Download Parameters", + "genomedl_parameters": { + "title": "genome-dl Parameters", "type": "object", "description": "", "default": "", @@ -116,6 +116,7 @@ "accession": { "type": "string", "description": "An NCBI Assembly accession to be downloaded", + "help": "Version-less accessions (e.g. GCF_000005845) are resolved to the latest version.", "fa_icon": "fas fa-font" }, "accessions": { @@ -127,12 +128,14 @@ "type": "string", "default": "fasta", "description": "Comma separated list of formats to download", + "help": "Choose from fasta, genbank, wgs, gff, gtf, protein, genpept, cds, translated-cds, rna, feature-table, assembly-report, assembly-stats or all.", "fa_icon": "fas fa-font" }, "section": { "type": "string", "default": "refseq", "description": "NCBI section to download", + "help": "Only applies to `--species`. Choose from refseq, genbank or all.", "fa_icon": "fas fa-font", "hidden": true }, @@ -140,26 +143,21 @@ "type": "string", "default": "complete", "description": "Comma separated list of assembly levels to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "kingdom": { - "type": "string", - "default": "bacteria", - "description": "Comma separated list of formats to download", + "help": "Only applies to `--species`. Choose from complete, chromosome, scaffold, contig or all.", "fa_icon": "fas fa-font", "hidden": true }, "limit": { - "type": "string", + "type": "integer", + "default": 100, "description": "Limit the number of assemblies to download", - "help": "If the the number of available genomes exceeds the given limit, a random subset will be selected.", - "fa_icon": "fas fa-font" + "help": "Only applies to `--species`, limit to first N assemblies returned by NCBI. Use 0 for no limit.", + "fa_icon": "fas fa-sort-numeric-up" }, - "keep_downloads": { + "genomedl_allow_outdated": { "type": "boolean", "default": false, - "description": "Save downloaded files into the bactopia-runs folder", + "description": "Download an explicitly requested outdated accession version instead of erroring", "fa_icon": "fas fa-toggle-on" } } @@ -517,7 +515,7 @@ "$ref": "#/$defs/mashtree_parameters" }, { - "$ref": "#/$defs/ncbigenomedownload_parameters" + "$ref": "#/$defs/genomedl_parameters" }, { "$ref": "#/$defs/optional_parameters" diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test b/workflows/bactopia-tools/mashtree/tests/main.nf.test index d928b0955..adca73ce4 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test @@ -40,4 +40,41 @@ nextflow_pipeline { ) } } + + test("Mashtree (accession) - haemophilus_influenzae|compressed_fasta") { + when { + params { + bactopia_test = "/species/haemophilus_influenzae/compressed" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + // Version-less accession, genome-dl resolves it to the latest version + accession = "GCF_020736045" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } } diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap index c4c13c7d1..4db668630 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap @@ -31,5 +31,38 @@ "nf-test": "0.9.5", "nextflow": "26.04.0" } + }, + "Mashtree (accession) - haemophilus_influenzae|compressed_fasta": { + "content": [ + 2, + [ + "bactopia-runs", + "bactopia-runs/mashtree", + "bactopia-runs/mashtree/logs", + "bactopia-runs/mashtree/logs/nf.command.begin", + "bactopia-runs/mashtree/logs/nf.command.err", + "bactopia-runs/mashtree/logs/nf.command.log", + "bactopia-runs/mashtree/logs/nf.command.out", + "bactopia-runs/mashtree/logs/nf.command.run", + "bactopia-runs/mashtree/logs/nf.command.sh", + "bactopia-runs/mashtree/logs/nf.command.trace", + "bactopia-runs/mashtree/logs/versions.yml", + "bactopia-runs/mashtree/mashtree.dnd", + "bactopia-runs/mashtree/mashtree.tsv", + "bactopia-runs/mashtree/nf-reports", + "bactopia-runs/mashtree/nf-reports/mashtree-dag.dot", + "bactopia-runs/mashtree/nf-reports/mashtree-report.html", + "bactopia-runs/mashtree/nf-reports/mashtree-timeline.html" + ], + [ + "versions.yml:md5,d8cd0c9b6f670d5ae21fda6592e85d32", + "mashtree.dnd:md5,02f89fd1a5f4a3a92df0b016061f67dd" + ] + ], + "timestamp": "2026-07-27T12:38:27.600224868", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/workflows/bactopia-tools/pangenome/main.nf b/workflows/bactopia-tools/pangenome/main.nf index b9cdcec96..2031a1131 100644 --- a/workflows/bactopia-tools/pangenome/main.nf +++ b/workflows/bactopia-tools/pangenome/main.nf @@ -8,17 +8,17 @@ * [Roary](https://github.com/sanger-pathogens/roary). It generates core-genome alignments * and gene presence/absence matrices, followed by SNP distance calculations. * You can supplement your pangenome with completed genomes using the --species or - * --accessions parameters, which downloads genomes from RefSeq and annotates them with - * Prokka. A phylogeny based on the core-genome alignment is created by IQ-Tree, with + * --accessions parameters, which downloads genomes from NCBI with genome-dl and annotates + * them with Prokka. A phylogeny based on the core-genome alignment is created by IQ-Tree, with * optional recombination masking using ClonalFrameML. Finally, pan-genome wide * association studies can be conducted using Scoary. * * @status stable * @keywords alignment, core-genome, pan-genome, phylogeny, comparative genomics, bactopia-tool * @tags complexity:complex input-type:parameter output-type:multiple features:bactopia-tool,aggregation,conditional-logic - * @citation clonalframeml, iqtree, iqtree_modelfinder, iqtree_ufboot, ncbigenomedownload, panaroo, pirate, prokka, roary, scoary + * @citation clonalframeml, genome_dl, iqtree, iqtree_modelfinder, iqtree_ufboot, panaroo, pirate, prokka, roary, scoary * - * @subworkflows utils_bactopia-tools, pangenome, ncbigenomedownload, prokka, clonalframeml, iqtree, scoary + * @subworkflows utils_bactopia-tools, pangenome, genomedl, prokka, clonalframeml, iqtree, scoary * * @input rundir * Directory containing results from a completed Bactopia analysis run @@ -30,10 +30,10 @@ * Use Roary as the pangenome tool instead of Panaroo * * @input species - * Species name used to supplement the pangenome with RefSeq assemblies + * Species name used to supplement the pangenome with NCBI assemblies * * @input accession - * Single NCBI Assembly RefSeq accession to supplement the pangenome + * Single NCBI Assembly accession to supplement the pangenome * * @input accessions * Path to a file listing NCBI Assembly accessions to supplement the pangenome @@ -119,7 +119,7 @@ params { } include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' -include { NCBIGENOMEDOWNLOAD } from '../../../subworkflows/ncbigenomedownload/main' +include { GENOMEDL } from '../../../subworkflows/genomedl/main' include { PROKKA } from '../../../subworkflows/prokka/main' include { PANGENOME } from '../../../subworkflows/pangenome/main' include { CLONALFRAMEML } from '../../../subworkflows/clonalframeml/main' @@ -135,9 +135,9 @@ workflow { // Download if applicable if (params.species || params.accession || params.accessions) { - ch_ncbigenomedownload = NCBIGENOMEDOWNLOAD(params.accessions) + ch_genomedl = GENOMEDL(params.accessions) ch_prokka = PROKKA( - ch_ncbigenomedownload.assemblies, + ch_genomedl.assemblies, params.prokka_proteins, params.prokka_prodigal_tf ) diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index a8476c710..15ca621da 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -28,7 +28,7 @@ includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" // Module specific config -includeConfig "../../../modules/ncbigenomedownload/module.config" +includeConfig "../../../modules/genomedl/module.config" includeConfig "../../../modules/prokka/module.config" includeConfig "../../../modules/pirate/module.config" includeConfig "../../../modules/roary/module.config" diff --git a/workflows/bactopia-tools/pangenome/nextflow_schema.json b/workflows/bactopia-tools/pangenome/nextflow_schema.json index 8c4b84ab1..048238349 100644 --- a/workflows/bactopia-tools/pangenome/nextflow_schema.json +++ b/workflows/bactopia-tools/pangenome/nextflow_schema.json @@ -42,8 +42,8 @@ } } }, - "ncbigenomedownload_parameters": { - "title": "NCBI Genome Download Parameters", + "genomedl_parameters": { + "title": "genome-dl Parameters", "type": "object", "description": "", "default": "", @@ -57,6 +57,7 @@ "accession": { "type": "string", "description": "An NCBI Assembly accession to be downloaded", + "help": "Version-less accessions (e.g. GCF_000005845) are resolved to the latest version.", "fa_icon": "fas fa-font" }, "accessions": { @@ -68,12 +69,14 @@ "type": "string", "default": "fasta", "description": "Comma separated list of formats to download", + "help": "Choose from fasta, genbank, wgs, gff, gtf, protein, genpept, cds, translated-cds, rna, feature-table, assembly-report, assembly-stats or all.", "fa_icon": "fas fa-font" }, "section": { "type": "string", "default": "refseq", "description": "NCBI section to download", + "help": "Only applies to `--species`. Choose from refseq, genbank or all.", "fa_icon": "fas fa-font", "hidden": true }, @@ -81,26 +84,21 @@ "type": "string", "default": "complete", "description": "Comma separated list of assembly levels to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "kingdom": { - "type": "string", - "default": "bacteria", - "description": "Comma separated list of formats to download", + "help": "Only applies to `--species`. Choose from complete, chromosome, scaffold, contig or all.", "fa_icon": "fas fa-font", "hidden": true }, "limit": { - "type": "string", + "type": "integer", + "default": 100, "description": "Limit the number of assemblies to download", - "help": "If the the number of available genomes exceeds the given limit, a random subset will be selected.", - "fa_icon": "fas fa-font" + "help": "Only applies to `--species`, limit to first N assemblies returned by NCBI. Use 0 for no limit.", + "fa_icon": "fas fa-sort-numeric-up" }, - "keep_downloads": { + "genomedl_allow_outdated": { "type": "boolean", "default": false, - "description": "Save downloaded files into the bactopia-runs folder", + "description": "Download an explicitly requested outdated accession version instead of erroring", "fa_icon": "fas fa-toggle-on" } } @@ -114,6 +112,7 @@ "properties": { "prokka_proteins": { "type": "string", + "default": "./data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, @@ -867,7 +866,7 @@ "$ref": "#/$defs/filter_parameters" }, { - "$ref": "#/$defs/ncbigenomedownload_parameters" + "$ref": "#/$defs/genomedl_parameters" }, { "$ref": "#/$defs/prokka_parameters" @@ -909,4 +908,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test b/workflows/bactopia-tools/pangenome/tests/main.nf.test index 53ba11679..2db6eaaea 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test @@ -83,6 +83,46 @@ nextflow_pipeline { } } + test("pangenome (panaroo --skip_recombination --accession) - multiple|portiera|compressed_gff") { + when { + params { + bactopia_test = "/species/mixed/gffs" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + accession = "GCF_000300035" + panaroo_core_threshold = 0.80 + panaroo_threshold = 0.85 + skip_recombination = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + // Ignore aligned_gene_sequences (panaroo gene naming is non-deterministic) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['**/aligned_gene_sequences/**']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + test("pangenome (pirate) - multiple|portiera|compressed_gff") { when { params { diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap index 6797f5c88..e0b224b6a 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap @@ -666,5 +666,88 @@ "nf-test": "0.9.5", "nextflow": "26.04.0" } + }, + "pangenome (panaroo --skip_recombination --accession) - multiple|portiera|compressed_gff": { + "content": [ + 5, + [ + "bactopia-runs", + "bactopia-runs/pangenome", + "bactopia-runs/pangenome/core-genome.distance.tsv", + "bactopia-runs/pangenome/core-genome.treefile", + "bactopia-runs/pangenome/iqtree", + "bactopia-runs/pangenome/iqtree/core-genome.alninfo.gz", + "bactopia-runs/pangenome/iqtree/core-genome.bionj", + "bactopia-runs/pangenome/iqtree/core-genome.ckp.gz", + "bactopia-runs/pangenome/iqtree/core-genome.contree", + "bactopia-runs/pangenome/iqtree/core-genome.iqtree", + "bactopia-runs/pangenome/iqtree/core-genome.log", + "bactopia-runs/pangenome/iqtree/core-genome.mldist", + "bactopia-runs/pangenome/iqtree/core-genome.splits.nex", + "bactopia-runs/pangenome/iqtree/core-genome.ufboot", + "bactopia-runs/pangenome/iqtree/logs", + "bactopia-runs/pangenome/iqtree/logs/nf.command.begin", + "bactopia-runs/pangenome/iqtree/logs/nf.command.err", + "bactopia-runs/pangenome/iqtree/logs/nf.command.log", + "bactopia-runs/pangenome/iqtree/logs/nf.command.out", + "bactopia-runs/pangenome/iqtree/logs/nf.command.run", + "bactopia-runs/pangenome/iqtree/logs/nf.command.sh", + "bactopia-runs/pangenome/iqtree/logs/nf.command.trace", + "bactopia-runs/pangenome/iqtree/logs/versions.yml", + "bactopia-runs/pangenome/nf-reports", + "bactopia-runs/pangenome/nf-reports/pangenome-dag.dot", + "bactopia-runs/pangenome/nf-reports/pangenome-report.html", + "bactopia-runs/pangenome/nf-reports/pangenome-timeline.html", + "bactopia-runs/pangenome/panaroo", + "bactopia-runs/pangenome/panaroo.aln.gz", + "bactopia-runs/pangenome/panaroo.filtered.aln.gz", + "bactopia-runs/pangenome/panaroo/aligned_gene_sequences", + "bactopia-runs/pangenome/panaroo/alignment_entropy.csv", + "bactopia-runs/pangenome/panaroo/combined_DNA_CDS.fasta.gz", + "bactopia-runs/pangenome/panaroo/combined_protein_CDS.fasta.gz", + "bactopia-runs/pangenome/panaroo/combined_protein_cdhit_out.txt", + "bactopia-runs/pangenome/panaroo/combined_protein_cdhit_out.txt.clstr", + "bactopia-runs/pangenome/panaroo/core_alignment_filtered_header.embl", + "bactopia-runs/pangenome/panaroo/core_alignment_header.embl", + "bactopia-runs/pangenome/panaroo/final_graph.gml.gz", + "bactopia-runs/pangenome/panaroo/gene_data.csv.gz", + "bactopia-runs/pangenome/panaroo/gene_presence_absence.Rtab", + "bactopia-runs/pangenome/panaroo/gene_presence_absence.csv", + "bactopia-runs/pangenome/panaroo/gene_presence_absence_roary.csv", + "bactopia-runs/pangenome/panaroo/logs", + "bactopia-runs/pangenome/panaroo/logs/nf.command.begin", + "bactopia-runs/pangenome/panaroo/logs/nf.command.err", + "bactopia-runs/pangenome/panaroo/logs/nf.command.log", + "bactopia-runs/pangenome/panaroo/logs/nf.command.out", + "bactopia-runs/pangenome/panaroo/logs/nf.command.run", + "bactopia-runs/pangenome/panaroo/logs/nf.command.sh", + "bactopia-runs/pangenome/panaroo/logs/nf.command.trace", + "bactopia-runs/pangenome/panaroo/logs/versions.yml", + "bactopia-runs/pangenome/panaroo/pan_genome_reference.fa.gz", + "bactopia-runs/pangenome/panaroo/pre_filt_graph.gml.gz", + "bactopia-runs/pangenome/panaroo/struct_presence_absence.Rtab", + "bactopia-runs/pangenome/panaroo/summary_statistics.txt", + "bactopia-runs/pangenome/snpdists", + "bactopia-runs/pangenome/snpdists/logs", + "bactopia-runs/pangenome/snpdists/logs/nf.command.begin", + "bactopia-runs/pangenome/snpdists/logs/nf.command.err", + "bactopia-runs/pangenome/snpdists/logs/nf.command.log", + "bactopia-runs/pangenome/snpdists/logs/nf.command.out", + "bactopia-runs/pangenome/snpdists/logs/nf.command.run", + "bactopia-runs/pangenome/snpdists/logs/nf.command.sh", + "bactopia-runs/pangenome/snpdists/logs/nf.command.trace", + "bactopia-runs/pangenome/snpdists/logs/versions.yml" + ], + [ + "versions.yml:md5,e01256842798c2b435032141a36e34a4", + "versions.yml:md5,5514295ba35a95ebb8417acd05766159", + "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" + ] + ], + "timestamp": "2026-07-27T13:10:28.183576616", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/workflows/bactopia-tools/prokka/nextflow_schema.json b/workflows/bactopia-tools/prokka/nextflow_schema.json index 17146b7be..75993c9d7 100644 --- a/workflows/bactopia-tools/prokka/nextflow_schema.json +++ b/workflows/bactopia-tools/prokka/nextflow_schema.json @@ -51,6 +51,7 @@ "properties": { "prokka_proteins": { "type": "string", + "default": "./data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, diff --git a/workflows/bactopia-tools/snippy/main.nf b/workflows/bactopia-tools/snippy/main.nf index 6e3b4d78e..0b88b0eab 100644 --- a/workflows/bactopia-tools/snippy/main.nf +++ b/workflows/bactopia-tools/snippy/main.nf @@ -12,7 +12,7 @@ * @tags complexity:complex input-type:parameter output-type:multiple features:bactopia-tool,comparative,phylogeny * @citation snippy, gubbins, iqtree * - * @subworkflows utils_bactopia-tools, ncbigenomedownload, snippy_run, snippy_core, gubbins, iqtree + * @subworkflows utils_bactopia-tools, genomedl, snippy_run, snippy_core, gubbins, iqtree * * @input rundir * Directory containing results from a completed Bactopia analysis run @@ -21,7 +21,7 @@ * Path to reference FASTA file for variant calling * * @input accession - * NCBI Assembly RefSeq accession to use as reference + * NCBI Assembly accession to download with genome-dl and use as reference * * @input snippy_core_mask * Path to BED file containing core genome regions @@ -74,7 +74,7 @@ params { } include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' -include { NCBIGENOMEDOWNLOAD } from '../../../subworkflows/ncbigenomedownload/main' +include { GENOMEDL } from '../../../subworkflows/genomedl/main' include { SNIPPY } from '../../../subworkflows/snippy/run/main' include { SNIPPY_CORE } from '../../../subworkflows/snippy/core/main' include { GUBBINS } from '../../../subworkflows/gubbins/main' @@ -91,8 +91,8 @@ workflow { if (params.reference) { ch_reference = params.reference } else if (params.accession) { - ch_ncbigenomedownload = NCBIGENOMEDOWNLOAD(null) - ch_reference = ch_ncbigenomedownload.reference + ch_genomedl = GENOMEDL(null) + ch_reference = ch_genomedl.reference } // Run Snippy per-sample diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 10309a4ef..713067b27 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -28,7 +28,7 @@ includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" // Module specific config -includeConfig "../../../modules/ncbigenomedownload/module.config" +includeConfig "../../../modules/genomedl/module.config" includeConfig "../../../modules/snippy/run/module.config" includeConfig "../../../modules/snippy/core/module.config" includeConfig "../../../modules/snpdists/module.config" diff --git a/workflows/bactopia-tools/snippy/nextflow_schema.json b/workflows/bactopia-tools/snippy/nextflow_schema.json index 07ce14cb2..ee9fb3668 100644 --- a/workflows/bactopia-tools/snippy/nextflow_schema.json +++ b/workflows/bactopia-tools/snippy/nextflow_schema.json @@ -42,8 +42,8 @@ } } }, - "ncbigenomedownload_parameters": { - "title": "NCBI Genome Download Parameters", + "genomedl_parameters": { + "title": "genome-dl Parameters", "type": "object", "description": "", "default": "", @@ -57,6 +57,7 @@ "accession": { "type": "string", "description": "An NCBI Assembly accession to be downloaded", + "help": "Version-less accessions (e.g. GCF_000005845) are resolved to the latest version.", "fa_icon": "fas fa-font" }, "accessions": { @@ -68,12 +69,14 @@ "type": "string", "default": "fasta", "description": "Comma separated list of formats to download", + "help": "Choose from fasta, genbank, wgs, gff, gtf, protein, genpept, cds, translated-cds, rna, feature-table, assembly-report, assembly-stats or all.", "fa_icon": "fas fa-font" }, "section": { "type": "string", "default": "refseq", "description": "NCBI section to download", + "help": "Only applies to `--species`. Choose from refseq, genbank or all.", "fa_icon": "fas fa-font", "hidden": true }, @@ -81,26 +84,21 @@ "type": "string", "default": "complete", "description": "Comma separated list of assembly levels to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "kingdom": { - "type": "string", - "default": "bacteria", - "description": "Comma separated list of formats to download", + "help": "Only applies to `--species`. Choose from complete, chromosome, scaffold, contig or all.", "fa_icon": "fas fa-font", "hidden": true }, "limit": { - "type": "string", + "type": "integer", + "default": 100, "description": "Limit the number of assemblies to download", - "help": "If the the number of available genomes exceeds the given limit, a random subset will be selected.", - "fa_icon": "fas fa-font" + "help": "Only applies to `--species`, limit to first N assemblies returned by NCBI. Use 0 for no limit.", + "fa_icon": "fas fa-sort-numeric-up" }, - "keep_downloads": { + "genomedl_allow_outdated": { "type": "boolean", "default": false, - "description": "Save downloaded files into the bactopia-runs folder", + "description": "Download an explicitly requested outdated accession version instead of erroring", "fa_icon": "fas fa-toggle-on" } } @@ -708,7 +706,7 @@ "$ref": "#/$defs/filter_parameters" }, { - "$ref": "#/$defs/ncbigenomedownload_parameters" + "$ref": "#/$defs/genomedl_parameters" }, { "$ref": "#/$defs/snippy_run_parameters" diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test b/workflows/bactopia-tools/snippy/tests/main.nf.test index a95ac07a1..6ff5850ed 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test @@ -226,4 +226,54 @@ nextflow_pipeline { ) } } + + test("Snippy (accession) - Mixed|compressed_fastq") { + when { + params { + bactopia_test = "/species/mixed/reads" + test_dataset = "" + test_dataset2 = "" + test_dataset3 = "" + test_r1 = "" + test_r2 = "" + test_se = "" + test_ont = "" + is_ci = true + outdir = "$outputDir" + // Take the reference from genome-dl instead of a local file. Snippy needs the + // annotations, so the download has to be GenBank rather than the default FASTA. + reference = null + accession = "GCF_000292685" + format = "genbank" + gubbins_min_window_size = 5000 + gubbins_filter_percentage = 100.0 + gubbins_iterations = 1 + snippy_mincov = 1 + snippy_minqual = 1 + snippy_basequal = 1 + snippy_mapqual = 1 + snippy_maxsoft = 1 + skip_recombination = true + skip_phylogeny = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: []) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: '.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } } diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap index 26797e33d..81f59e17a 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap @@ -1566,5 +1566,294 @@ "nf-test": "0.9.5", "nextflow": "26.04.0" } + }, + "Snippy (accession) - Mixed|compressed_fastq": { + "content": [ + 10, + [ + "ERR1438863", + "ERR1438863/tools", + "ERR1438863/tools/snippy", + "ERR1438863/tools/snippy/GCF_000292685", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.aligned.fa.gz", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.annotated.vcf.gz", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.bam", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.bam.bai", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.bed.gz", + "ERR1438863/tools/snippy/GCF_000292685/ERR1438863.consensus.fa.gz", + 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"prokka_proteins": { "type": "string", - "default": "${projectDir}/data/proteins.faa", + "default": "./data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font", "hidden": true From b6557187d3294611eb56dee1ea6b9a0a30f3895f Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 14:33:33 -0600 Subject: [PATCH 20/43] add bactopia_dir param for relative paths (e.g. prokka_proteins) --- .../docs/project/01-repository-structure.md | 4 +-- .../docs/standards/05-module-documentation.md | 12 +++++++ CHANGELOG.md | 8 +++++ modules/prokka/module.config | 2 +- modules/prokka/schema.json | 2 +- modules/prokka/tests/main.nf.test | 36 +++++++++++++++++++ modules/prokka/tests/main.nf.test.snap | 22 ++++++++++++ modules/prokka/tests/nextflow.config | 2 ++ nextflow.config | 3 ++ nextflow_schema.json | 2 +- subworkflows/prokka/tests/nextflow.config | 2 ++ .../bactopia-tools/abricate/nextflow.config | 3 ++ .../bactopia-tools/abritamr/nextflow.config | 3 ++ .../bactopia-tools/agrvate/nextflow.config | 3 ++ .../amrfinderplus/nextflow.config | 3 ++ .../bactopia-tools/ariba/nextflow.config | 3 ++ .../bactopia-tools/bakta/nextflow.config | 3 ++ .../bactopia-tools/blastn/nextflow.config | 3 ++ .../bactopia-tools/blastp/nextflow.config | 3 ++ .../bactopia-tools/blastx/nextflow.config | 3 ++ .../bactopia-tools/bracken/nextflow.config | 3 ++ .../bactopia-tools/btyper3/nextflow.config | 3 ++ .../bactopia-tools/busco/nextflow.config | 3 ++ .../bactopia-tools/checkm/nextflow.config | 3 ++ .../bactopia-tools/checkm2/nextflow.config | 3 ++ .../clermontyping/nextflow.config | 3 ++ .../defensefinder/nextflow.config | 3 ++ .../bactopia-tools/ectyper/nextflow.config | 3 ++ .../bactopia-tools/eggnog/nextflow.config | 3 ++ .../bactopia-tools/emmtyper/nextflow.config | 3 ++ .../bactopia-tools/fastani/nextflow.config | 3 ++ .../bactopia-tools/gamma/nextflow.config | 3 ++ .../bactopia-tools/gamma/nextflow_schema.json | 2 +- .../bactopia-tools/genotyphi/nextflow.config | 3 ++ .../bactopia-tools/gigatyper/nextflow.config | 3 ++ workflows/bactopia-tools/gtdb/nextflow.config | 3 ++ .../bactopia-tools/hicap/nextflow.config | 3 ++ .../bactopia-tools/hpsuissero/nextflow.config | 3 ++ .../bactopia-tools/ismapper/nextflow.config | 3 ++ .../bactopia-tools/kleborate/nextflow.config | 3 ++ .../bactopia-tools/kraken2/nextflow.config | 3 ++ .../bactopia-tools/legsta/nextflow.config | 3 ++ .../bactopia-tools/lissero/nextflow.config | 3 ++ .../bactopia-tools/mashdist/nextflow.config | 3 ++ .../bactopia-tools/mashtree/nextflow.config | 3 ++ .../bactopia-tools/mcroni/nextflow.config | 3 ++ .../meningotype/nextflow.config | 3 ++ .../bactopia-tools/merlin/nextflow.config | 3 ++ .../bactopia-tools/midas/nextflow.config | 3 ++ workflows/bactopia-tools/mlst/nextflow.config | 3 ++ .../bactopia-tools/mobsuite/nextflow.config | 3 ++ .../bactopia-tools/mykrobe/nextflow.config | 3 ++ .../bactopia-tools/ngmaster/nextflow.config | 3 ++ .../bactopia-tools/pangenome/nextflow.config | 3 ++ .../pangenome/nextflow_schema.json | 2 +- .../bactopia-tools/pasty/nextflow.config | 3 ++ .../bactopia-tools/pbptyper/nextflow.config | 3 ++ .../bactopia-tools/phispy/nextflow.config | 3 ++ .../phispy/nextflow_schema.json | 2 +- .../plasmidfinder/nextflow.config | 3 ++ .../bactopia-tools/pneumocat/nextflow.config | 3 ++ .../bactopia-tools/prokka/nextflow.config | 3 ++ .../prokka/nextflow_schema.json | 2 +- .../bactopia-tools/quast/nextflow.config | 3 ++ workflows/bactopia-tools/rgi/nextflow.config | 3 ++ .../bactopia-tools/sccmec/nextflow.config | 3 ++ .../bactopia-tools/scrubber/nextflow.config | 3 ++ .../bactopia-tools/seqsero2/nextflow.config | 3 ++ .../bactopia-tools/seroba/nextflow.config | 3 ++ .../bactopia-tools/shigapass/nextflow.config | 3 ++ .../bactopia-tools/shigatyper/nextflow.config | 3 ++ .../shigeifinder/nextflow.config | 3 ++ .../bactopia-tools/sistr/nextflow.config | 3 ++ .../bactopia-tools/snippy/nextflow.config | 3 ++ .../bactopia-tools/spatyper/nextflow.config | 3 ++ .../bactopia-tools/ssuissero/nextflow.config | 3 ++ .../bactopia-tools/staphscan/nextflow.config | 3 ++ .../bactopia-tools/staphtyper/nextflow.config | 3 ++ .../bactopia-tools/stecfinder/nextflow.config | 3 ++ .../bactopia-tools/stxtyper/nextflow.config | 7 ++-- .../bactopia-tools/sylph/nextflow.config | 3 ++ .../bactopia-tools/tblastn/nextflow.config | 3 ++ .../bactopia-tools/tblastx/nextflow.config | 3 ++ .../bactopia-tools/tbprofiler/nextflow.config | 3 ++ .../bactopia-tools/traitar/nextflow.config | 3 ++ .../traitar/nextflow_schema.json | 5 +-- workflows/cleanyerreads/nextflow.config | 3 ++ workflows/staphopia/nextflow.config | 3 ++ workflows/staphopia/nextflow_schema.json | 2 +- workflows/teton/nextflow.config | 3 ++ 90 files changed, 319 insertions(+), 14 deletions(-) diff --git a/.claude/docs/project/01-repository-structure.md b/.claude/docs/project/01-repository-structure.md index 13e33678c..b1bb8fd96 100644 --- a/.claude/docs/project/01-repository-structure.md +++ b/.claude/docs/project/01-repository-structure.md @@ -87,10 +87,10 @@ bactopia/ - **Contents**: - `conda/` - Development environment specifications - `citations.yml` - Tool citations and references - - `proteins.faa` - Protein reference file + - `proteins.faa` - Trusted protein reference used by Prokka (`--prokka_proteins`) - Image assets (logos, banners) -Note: `catalog.json` (auto-generated component catalog) and `llms.txt` (AI discovery index) live at the repo root, not under `data/`. +Note: `catalog.json` (auto-generated component catalog) and `llms.txt` (AI discovery index) live at the repo root, not under `data/`. Modules never ship their own data — vendored static files live here and are referenced from `module.config` via `${params.bactopia_dir}`; downloadable databases go through a `download`/`fetch` submodule instead. ### `/bin/` - **Purpose**: CLI wrapper scripts for the bioconda `bactopia` package diff --git a/.claude/docs/standards/05-module-documentation.md b/.claude/docs/standards/05-module-documentation.md index 6d77df7b7..d28aec436 100644 --- a/.claude/docs/standards/05-module-documentation.md +++ b/.claude/docs/standards/05-module-documentation.md @@ -762,6 +762,18 @@ process { - First line is a section comment using the module name in snake_case: `// {tool}` or `// {tool}_{process}` - Modules with no parameters use `// No parameters` (capital N) - `fa_icon` in schema.json is determined by type: `string` = `fas fa-font`, `integer` = `fas fa-hashtag`, `number` = `fas fa-percentage`, `boolean` = `fas fa-toggle-on` +- **Modules never ship their own data.** There is no `modules/{tool}/data/` directory in this + repo, and adding one is not the pattern: downloadable databases go through a + `download`/`fetch` submodule (see `bakta`, `checkm2`, `deacon`, `eggnog`, `gtdbtk`, `midas`, + `nohuman`, `traitar`), and the one vendored static file lives at the repo root in `data/` +- Paths to that **vendored data** must be anchored on `${params.bactopia_dir}` (the repo root, + emitted into every generated workflow `nextflow.config`), e.g. + `prokka_proteins = "${params.bactopia_dir}/data/proteins.faa"`. A bare relative path such as + `"./data/proteins.faa"` resolves against **launchDir**, not the module, and `${projectDir}` + differs per tier. Enforced by lint rule `MC016`; the matching workflow-side anchor is + enforced by `W022`. Component `tests/nextflow.config` files that include such a + `module.config` must define `bactopia_dir = "${projectDir}/../../.."` (under nf-test, + `projectDir` is the `tests/` directory) ### 10.2 Key Properties diff --git a/CHANGELOG.md b/CHANGELOG.md index b99475e4d..a57702d75 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,10 +40,18 @@ sidebar_position: 5000 - Deacon modules now use bactopia-teton container instead of standalone deacon container - Teton and scrubber workflows default to deacon instead of nohuman for host read removal - cleanyerreads workflow supports `--use_deacon` flag for host read removal +- Every generated workflow `nextflow.config` now declares `params.bactopia_dir`, an absolute + anchor to the Bactopia repo root, so `module.config` can reference vendored data under + `data/` regardless of tier or launch directory ### `Fixed` - float parameters being interpreted as strings in CLI +- `--prokka_proteins` defaulting to `./data/proteins.faa`, which Nextflow resolves against the + launch directory rather than the repo. Only runs launched from the repo root picked up the + bundled protein set; every other run failed with + `Input file './data/proteins.faa' does not exist`. The default is now anchored on the new + `params.bactopia_dir` and resolves to `data/proteins.faa` from any working directory ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/modules/prokka/module.config b/modules/prokka/module.config index a4efb615f..3be4f7163 100644 --- a/modules/prokka/module.config +++ b/modules/prokka/module.config @@ -6,7 +6,7 @@ params { prokka_debug = false prokka_evalue = "1e-09" prokka_opts = "" - prokka_proteins = "./data/proteins.faa" + prokka_proteins = "${params.bactopia_dir}/data/proteins.faa" } process { diff --git a/modules/prokka/schema.json b/modules/prokka/schema.json index 1ec19aa52..9ba072eee 100644 --- a/modules/prokka/schema.json +++ b/modules/prokka/schema.json @@ -14,7 +14,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "./data/proteins.faa", + "default": "${params.bactopia_dir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, diff --git a/modules/prokka/tests/main.nf.test b/modules/prokka/tests/main.nf.test index 916f3ed46..48867f3ad 100644 --- a/modules/prokka/tests/main.nf.test +++ b/modules/prokka/tests/main.nf.test @@ -70,4 +70,40 @@ nextflow_process { ) } } + + test("prokka - module - SRR2838702 - bundled proteins default") { + // Exercises the shipped prokka_proteins default rather than overriding it. + // The default is anchored on params.bactopia_dir, so this fails if the + // anchor is wrong or the vendored FASTA is missing. + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "SRR2838702"], + fna: file("${params.test_data_dir}/datasets/generic/GCF_000292685.fna") + ) + ) + input[1] = file(params.prokka_proteins, checkIfExists: true) + input[2] = null + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.txt, + record.tsv, + record.versions + ).match() } + ) + } + } } diff --git a/modules/prokka/tests/main.nf.test.snap b/modules/prokka/tests/main.nf.test.snap index c83b3ff4a..1d3aaab97 100644 --- a/modules/prokka/tests/main.nf.test.snap +++ b/modules/prokka/tests/main.nf.test.snap @@ -42,5 +42,27 @@ "nf-test": "0.9.5", "nextflow": "26.04.0" } + }, + "prokka - module - SRR2838702 - bundled proteins default": { + "content": [ + { + "id": "SRR2838702-PROKKA", + "logs_dir": "SRR2838702/main/annotator/prokka/logs/", + "name": "SRR2838702", + "output_dir": "SRR2838702/main/annotator/prokka/", + "process_name": "prokka", + "scope": "sample" + }, + "SRR2838702.txt:md5,09c05b70e569b8397697494b799fe2b0", + "SRR2838702.tsv:md5,64e127d52999b87519920aaf519c6947", + [ + "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" + ] + ], + "timestamp": "2026-07-27T14:10:11.585993926", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/prokka/tests/nextflow.config b/modules/prokka/tests/nextflow.config index b294bc373..a3ef0d7c6 100644 --- a/modules/prokka/tests/nextflow.config +++ b/modules/prokka/tests/nextflow.config @@ -12,6 +12,8 @@ params { bactopia_version = '4.0.0' bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + // Under nf-test, projectDir is this tests/ directory + bactopia_dir = "${projectDir}/../../.." condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name merge_folder = "merged-results" diff --git a/nextflow.config b/nextflow.config index c034d1db4..20065c0e1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,6 +23,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}" includeConfig "./conf/params.config" includeConfig "./conf/params/bactopia.config" diff --git a/nextflow_schema.json b/nextflow_schema.json index ece72f94c..8bdd973c6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1008,7 +1008,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "./data/proteins.faa", + "default": "${params.bactopia_dir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font", "hidden": true diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index 153eae26c..b5e731197 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -11,6 +11,8 @@ params { } bactopia_version = '4.0.0' bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + // Under nf-test, projectDir is this tests/ directory + bactopia_dir = "${projectDir}/../../.." condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name merge_folder = "merged-results" diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index 5c17ed5e2..3d09126ad 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 0723f02b2..d624b2859 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index accab6c24..f87f0a9a3 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index f8ed3bf45..d3fa3d0d6 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index 98fd0e4b9..a542b7414 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 405a16ffe..6019eaab8 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index 5224360b4..f9275250b 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 87cd40c7c..2c8003e73 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index b00135147..502076a53 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index cc671fbe1..98e288684 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index 30c7957bc..aebe64002 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index f7213715b..67a26c36d 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index 4f64f7a21..ba72bd69b 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 79771ed5d..5c0dec559 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index d459b8145..84a35d6ed 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index bfe8f90e8..7a1617211 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 69b20ef12..8fab9475d 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index 16dbdf394..de3d39935 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index d4d845927..dc4b791d9 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index 2192e7505..ecbca2b94 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index fab2ece18..cf60cdb01 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/gamma/nextflow_schema.json b/workflows/bactopia-tools/gamma/nextflow_schema.json index bebfebbf7..d0c9da3f6 100644 --- a/workflows/bactopia-tools/gamma/nextflow_schema.json +++ b/workflows/bactopia-tools/gamma/nextflow_schema.json @@ -478,4 +478,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index 0a4699400..f905d9462 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index 0f0bf0302..d20c34106 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index b3c5e9737..c46593d5a 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index ccf0cbf73..5f461769b 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index c46376282..2df6bb4da 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 3a2019366..2f9ec1016 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index 5dc25af71..7e1390d2e 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index e85ecf0ae..e7d85b184 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index bd5a68d94..7c384f704 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index 97e6ac23a..02cd2040c 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index b4cefb47f..ff07b93e4 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index 1ecd73c78..c6808120e 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index ade53db3e..26af1ef1c 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index 0c1d8f1ff..9be7071d8 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index a826d2996..15f0587b9 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index 301b33fe0..fbb77c843 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index 6901330ea..a1cd2b7ff 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index 93ba6d3bf..12cda34b1 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index 8bc658a00..60e85dc52 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 5e873074b..fa4dfd990 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index 15ca621da..ef21927f6 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/pangenome/nextflow_schema.json b/workflows/bactopia-tools/pangenome/nextflow_schema.json index 048238349..a521917fd 100644 --- a/workflows/bactopia-tools/pangenome/nextflow_schema.json +++ b/workflows/bactopia-tools/pangenome/nextflow_schema.json @@ -112,7 +112,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "./data/proteins.faa", + "default": "${params.bactopia_dir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index 37243b1fd..e025970b1 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index 12421f574..e0c20ca3d 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index 38ccbba70..e1efd97b1 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/phispy/nextflow_schema.json b/workflows/bactopia-tools/phispy/nextflow_schema.json index 8ce9406d3..1318a4cce 100644 --- a/workflows/bactopia-tools/phispy/nextflow_schema.json +++ b/workflows/bactopia-tools/phispy/nextflow_schema.json @@ -483,4 +483,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} +} \ No newline at end of file diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 3ea635a51..9c1bca127 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index 97395f464..3847fbbdb 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index cc96db7b8..4d2a78469 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/prokka/nextflow_schema.json b/workflows/bactopia-tools/prokka/nextflow_schema.json index 75993c9d7..b0ecbba9a 100644 --- a/workflows/bactopia-tools/prokka/nextflow_schema.json +++ b/workflows/bactopia-tools/prokka/nextflow_schema.json @@ -51,7 +51,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "./data/proteins.faa", + "default": "${params.bactopia_dir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font" }, diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 4efd351fe..68a7f4582 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index cb0624296..f4aa4d367 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index a98c88393..bf0ea381f 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index 3cae14963..330cc209e 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index 323206894..b577cfe5b 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index 6124b6639..a461f7ec3 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 67def7e3d..c23c6564b 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index acab21ce7..64694332c 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 2477af508..0040ec10f 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index cb29ec1fd..e6461b336 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 713067b27..61d6febc1 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index 479a0f8b9..519c421f8 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 3fd2bde6e..9358ac1da 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index bbfd45818..83b4c7330 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index cb945184e..c30928f5c 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index 3bbd78b12..b2d596299 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/stxtyper/nextflow.config b/workflows/bactopia-tools/stxtyper/nextflow.config index 41fe903fe..fa62e8f45 100644 --- a/workflows/bactopia-tools/stxtyper/nextflow.config +++ b/workflows/bactopia-tools/stxtyper/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" @@ -83,9 +86,9 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.5' + id 'nf-bactopia@2.1.6' } bactopia { parametersSchema = "${projectDir}/nextflow_schema.json" -} \ No newline at end of file +} diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 4460026eb..41dad8235 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index aec6f670c..1b04e2a15 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 6d16650c6..11ab0ea1a 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 5778e21b9..91473f848 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index f0e42e9e6..a86378106 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -24,6 +24,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../../.." includeConfig "../../../conf/params.config" includeConfig "../../../conf/params/bactopia-tools.config" diff --git a/workflows/bactopia-tools/traitar/nextflow_schema.json b/workflows/bactopia-tools/traitar/nextflow_schema.json index d5a98c57c..623157972 100644 --- a/workflows/bactopia-tools/traitar/nextflow_schema.json +++ b/workflows/bactopia-tools/traitar/nextflow_schema.json @@ -52,7 +52,8 @@ "traitar_db": { "type": "string", "description": "Path a Traitar database (should contain the Pfam-A.hmm file)", - "fa_icon": "fas fa-font" + "fa_icon": "fas fa-font", + "is_required": true }, "download_traitar": { "type": "boolean", @@ -449,4 +450,4 @@ "$ref": "#/$defs/generic_parameters" } ] -} +} \ No newline at end of file diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index e0bfcc125..cf8325fbf 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -23,6 +23,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../.." includeConfig "../../conf/params.config" includeConfig "../../conf/params/bactopia.config" diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index f5ad70e5d..d8b32a034 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -23,6 +23,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../.." includeConfig "../../conf/params.config" includeConfig "../../conf/params/bactopia.config" diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index d02358d7a..76cfce481 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -1003,7 +1003,7 @@ "properties": { "prokka_proteins": { "type": "string", - "default": "./data/proteins.faa", + "default": "${params.bactopia_dir}/data/proteins.faa", "description": "FASTA file of trusted proteins to first annotate from", "fa_icon": "fas fa-font", "hidden": true diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 7e27d77ac..d2da6c557 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -23,6 +23,9 @@ manifest.version = "${params.bactopia_version}" // Includes params.bactopia_cache = env("BACTOPIA_CACHEDIR") ? "${env('BACTOPIA_CACHEDIR')}" : "${env('HOME')}/.bactopia" +// Absolute anchor to the Bactopia repo root, used by module.config to locate +// vendored data under data/ (a relative path would resolve against launchDir) +params.bactopia_dir = "${projectDir}/../.." includeConfig "../../conf/params.config" includeConfig "../../conf/params/bactopia.config" From 224a009f0940e6a061e8fba89d1efb56f4c49d8a Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 14:53:54 -0600 Subject: [PATCH 21/43] replace ncbigenomedownload with genome-dl --- .claude/docs/reference/01-examples.md | 4 +- catalog.json | 100 +--------------- conf/test-times.json | 8 -- data/citations.yml | 7 -- llms.txt | 2 +- modules/bactopia/gather/main.nf | 2 +- modules/ncbigenomedownload/main.nf | 113 ------------------ modules/ncbigenomedownload/module.config | 47 -------- modules/ncbigenomedownload/schema.json | 77 ------------ modules/ncbigenomedownload/tests/main.nf.test | 36 ------ .../tests/main.nf.test.snap | 25 ---- .../ncbigenomedownload/tests/nextflow.config | 39 ------ .../ncbigenomedownload/tests/nf-test.config | 11 -- subworkflows/bactopia/gather/main.nf | 2 +- subworkflows/ncbigenomedownload/main.nf | 67 ----------- .../ncbigenomedownload/tests/.nftignore | 2 - .../ncbigenomedownload/tests/main.nf.test | 35 ------ .../tests/main.nf.test.snap | 25 ---- .../ncbigenomedownload/tests/nextflow.config | 39 ------ .../ncbigenomedownload/tests/nf-test.config | 11 -- 20 files changed, 6 insertions(+), 646 deletions(-) delete mode 100644 modules/ncbigenomedownload/main.nf delete mode 100644 modules/ncbigenomedownload/module.config delete mode 100644 modules/ncbigenomedownload/schema.json delete mode 100644 modules/ncbigenomedownload/tests/main.nf.test delete mode 100644 modules/ncbigenomedownload/tests/main.nf.test.snap delete mode 100644 modules/ncbigenomedownload/tests/nextflow.config delete mode 100644 modules/ncbigenomedownload/tests/nf-test.config delete mode 100644 subworkflows/ncbigenomedownload/main.nf delete mode 100644 subworkflows/ncbigenomedownload/tests/.nftignore delete mode 100644 subworkflows/ncbigenomedownload/tests/main.nf.test delete mode 100644 subworkflows/ncbigenomedownload/tests/main.nf.test.snap delete mode 100644 subworkflows/ncbigenomedownload/tests/nextflow.config delete mode 100644 subworkflows/ncbigenomedownload/tests/nf-test.config diff --git a/.claude/docs/reference/01-examples.md b/.claude/docs/reference/01-examples.md index 24f77797b..9c2ca9798 100644 --- a/.claude/docs/reference/01-examples.md +++ b/.claude/docs/reference/01-examples.md @@ -174,9 +174,9 @@ workflow MLST { * @status stable * @keywords alignment, core-genome, pan-genome, phylogeny, comparative genomics, bactopia-tool * @tags complexity:complex input-type:parameter output-type:multiple features:bactopia-tool,aggregation,conditional-logic - * @citation clonalframeml, iqtree, iqtree_modelfinder, iqtree_ufboot, ncbigenomedownload, panaroo, pirate, prokka, roary, scoary + * @citation clonalframeml, iqtree, iqtree_modelfinder, iqtree_ufboot, genome_dl, panaroo, pirate, prokka, roary, scoary * - * @subworkflows utils_bactopia-tools, pangenome, ncbigenomedownload, prokka, clonalframeml, iqtree, scoary + * @subworkflows utils_bactopia-tools, pangenome, genome_dl, prokka, clonalframeml, iqtree, scoary * * @input rundir * Directory containing results from a completed Bactopia analysis run diff --git a/catalog.json b/catalog.json index 29e74293d..c8e8c8aea 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-07-27T18:54:11Z", + "generated": "2026-07-27T20:46:58Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.2.0", "nf_bactopia_version": "2.1.6", @@ -1949,58 +1949,6 @@ ] } }, - "ncbigenomedownload": { - "description": "Download assemblies and annotation files from NCBI's Assembly database.", - "path": "modules/ncbigenomedownload/", - "scope": "run", - "process_name": "ncbigenomedownload", - "tool": { - "name": "ncbi-genome-download", - "version": "0.3.3" - }, - "emits": [ - "gbff", - "fna", - "rm", - "features", - "gff", - "faa", - "gpff", - "wgs_gbk", - "cds", - "rna", - "rna_fna", - "report", - "stats", - "accessions" - ], - "emits_optional": [ - "gbff", - "fna", - "rm", - "features", - "gff", - "faa", - "gpff", - "wgs_gbk", - "cds", - "rna", - "rna_fna", - "report", - "stats", - "accessions" - ], - "tags": { - "complexity": "moderate", - "input_type": "single", - "output_type": "multiple", - "features": [ - "internet-access", - "resource-download", - "conditional-logic" - ] - } - }, "ngmaster": { "description": "Serotyping and Multi-Antigen Sequence Typing (MAST) of *Neisseria gonorrhoeae*.", "path": "modules/ngmaster/", @@ -5083,52 +5031,6 @@ ] } }, - "ncbigenomedownload": { - "description": "Download bacterial genomes from NCBI's RefSeq database.", - "path": "subworkflows/ncbigenomedownload/", - "takes_params": [ - "accessions" - ], - "emits": { - "sample_outputs": [ - "gbff", - "fna", - "gff", - "faa", - "gpff", - "wgs_gbk", - "cds", - "rna", - "rna_fna", - "features", - "rm", - "report", - "stats", - "accessions" - ], - "bactopia_tools": [], - "run_outputs": [], - "assemblies": [ - "fna" - ], - "reference": [] - }, - "scope": "sample", - "calls": { - "modules": [ - "ncbigenomedownload" - ] - }, - "tags": { - "complexity": "moderate", - "input_type": "single", - "output_type": "multiple", - "features": [ - "resource-download", - "database-dependent" - ] - } - }, "ngmaster": { "description": "Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.", "path": "subworkflows/ngmaster/", diff --git a/conf/test-times.json b/conf/test-times.json index a9c064f12..1ca07af5f 100644 --- a/conf/test-times.json +++ b/conf/test-times.json @@ -221,10 +221,6 @@ "expected_seconds": 24.1, "tolerance_factor": 2.0 }, - "modules/ncbigenomedownload": { - "expected_seconds": 44.4, - "tolerance_factor": 2.0 - }, "modules/ngmaster": { "expected_seconds": 86.1, "tolerance_factor": 2.0 @@ -549,10 +545,6 @@ "expected_seconds": 28.5, "tolerance_factor": 2.0 }, - "subworkflows/ncbigenomedownload": { - "expected_seconds": 39.5, - "tolerance_factor": 2.0 - }, "subworkflows/ngmaster": { "expected_seconds": 42.5, "tolerance_factor": 2.0 diff --git a/data/citations.yml b/data/citations.yml index 1c0df9838..84517d17a 100644 --- a/data/citations.yml +++ b/data/citations.yml @@ -700,13 +700,6 @@ tools: cite: | Steinig E [Nanoq: Minimal but speedy quality control for nanopore reads in Rust](https://github.com/esteinig/nanoq) (GitHub) - ncbigenomedownload: - name: ncbi-genome-download - link: https://github.com/kblin/ncbi-genome-download - description: Scripts to download genomes from the NCBI FTP servers - cite: | - Blin K [ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers](https://github.com/kblin/ncbi-genome-download) (GitHub) - nextflow: name: Nextflow provenance_only: true diff --git a/llms.txt b/llms.txt index 55cefec6f..be1811c88 100644 --- a/llms.txt +++ b/llms.txt @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -106 tool-specific modules live under `modules/`. Each module directory contains: +105 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/bactopia/gather/main.nf b/modules/bactopia/gather/main.nf index 4df3b7399..278849c5d 100644 --- a/modules/bactopia/gather/main.nf +++ b/modules/bactopia/gather/main.nf @@ -14,7 +14,7 @@ * @status stable * @keywords fastq, validation, sra, ena, download, merging, simulation, art, ncbi * @tags complexity:complex input-type:multiple output-type:multiple features:internet-access,resource-download,conditional-logic - * @citation bactopia, art, fastq_dl, fastq_scan, ncbigenomedownload, pigz + * @citation bactopia, art, fastq_dl, fastq_scan, genome_dl, pigz * * @input record(meta, r1_files, r2_files, se_files, lr_files, fna_files) * - `meta`: Groovy Record containing sample information diff --git a/modules/ncbigenomedownload/main.nf b/modules/ncbigenomedownload/main.nf deleted file mode 100644 index c3b2da8c7..000000000 --- a/modules/ncbigenomedownload/main.nf +++ /dev/null @@ -1,113 +0,0 @@ -/** - * Download assemblies and annotation files from NCBI's Assembly database. - * - * Uses [ncbi-genome-download](https://github.com/kblin/ncbi-genome-download) to efficiently fetch - * one or more complete genome assemblies and their associated annotation and report files from - * the NCBI FTP site based on accession numbers, species name, or assembly ID. - * - * @status stable - * @keywords ncbi, download, genome, assembly, fasta, genbank, utility - * @tags complexity:moderate input-type:single output-type:multiple features:internet-access,resource-download,conditional-logic - * @citation ncbigenomedownload - * - * @input accessions? - * A path to a text file containing a list of NCBI Assembly accession numbers (one per line) - * - * @output record(meta, gbff?, fna?, rm?, features?, gff?, faa?, gpff?, wgs_gbk?, cds?, rna?, rna_fna?, report?, stats?, accessions?, results, logs, nf_logs, versions) - * - `gbff?`: GenBank format of the genomic sequence(s) (*_genomic.gbff.gz) - * - `fna?`: FASTA format of the genomic nucleotide sequence(s) (*_genomic.fna.gz) - * - `rm?`: RepeatMasker output for eukaryotes - * - `features?`: Tab-delimited text file reporting locations and attributes for a subset of features - * - `gff?`: Annotation of the genomic sequence(s) in GFF3 format (*_genomic.gff.gz) - * - `faa?`: FASTA format of the accessioned protein products (*_protein.faa.gz) - * - `gpff?`: GenPept format of the accessioned protein products - * - `wgs_gbk?`: GenBank flat file format of the WGS master - * - `cds?`: FASTA format of the nucleotide sequences corresponding to all CDS features - * - `rna?`: FASTA format of accessioned RNA products - * - `rna_fna?`: FASTA format of the nucleotide sequences corresponding to all RNA features - * - `report?`: Tab-delimited text file reporting assembly unit names, roles, and relationships - * - `stats?`: Tab-delimited text file reporting assembly statistics - * - `accessions?`: The generated accession list files - */ -nextflow.enable.types = true - -// bactopia-lint: ignore M017,M026 -process NCBIGENOMEDOWNLOAD { - label 'process_low' - - conda "${task.ext.condaDir}/${task.ext.toolName}" - container "${task.ext.container}" - - input: - accessions : Path? - - output: - record( - // Named fields (used downstream) - meta: meta, - gbff: files("*_genomic.gbff.gz", optional: true), - fna: files("*_genomic.fna.gz", optional: true), - rm: files("*_rm.out.gz", optional: true), - features: files("*_feature_table.txt.gz", optional: true), - gff: files("*_genomic.gff.gz", optional: true), - faa: files("*_protein.faa.gz", optional: true), - gpff: files("*_protein.gpff.gz", optional: true), - wgs_gbk: files("*_wgsmaster.gbff.gz", optional: true), - cds: files("*_cds_from_genomic.fna.gz", optional: true), - rna: files("*_rna.fna.gz", optional: true), - rna_fna: files("*_rna_from_genomic.fna.gz", optional: true), - report: files("*_assembly_report.txt", optional: true), - stats: files("*_assembly_stats.txt", optional: true), - accessions: files("accession-*.txt", optional: true), - // Generic fields (used for publishing) - results: [ - files("*.gz", optional: true), - files("*.txt", optional: true) - ], - logs: files("*.{log,err}", optional: true), - nf_logs: files(".command.*"), - versions: files("versions.yml") - ) - - script: - meta = record( - id: task.ext.meta_id, - name: task.ext.meta_id, - limit: task.ext.meta_limit, - accession: task.ext.meta_accession, - species: task.ext.meta_species, - scope: task.ext.scope, - process_name: task.ext.process_name, - output_dir: task.ext.process_name, - logs_dir: "${task.ext.process_name}/logs" - ) - - def has_accessions = accessions ? true : false - def opts = "${task.ext.args} --output-folder ./ --flat-output -p ${task.cpus} -r ${task.ext.max_retry}" - """ - if [ "${meta.species}" != "null" ]; then - if [ "${meta.limit}" != "null" ]; then - ncbi-genome-download ${opts} -g "${meta.species}" --dry-run | grep -v "Considering" > accession-list.txt - shuf accession-list.txt | head -n ${meta.limit} | cut -f 1,1 > accession-subset.txt - ncbi-genome-download ${opts} -u "https://ftp.ncbi.nlm.nih.gov/genomes" -A accession-subset.txt - else - ncbi-genome-download ${opts} -g "${meta.species}" - fi - fi - - if [ "${meta.accession}" != "null" ]; then - ncbi-genome-download ${opts} -u "https://ftp.ncbi.nlm.nih.gov/genomes" -A ${meta.accession} - fi - - if [ "${has_accessions}" == "true" ]; then - ncbi-genome-download ${opts} -u "https://ftp.ncbi.nlm.nih.gov/genomes" -A ${accessions} - fi - - # Cleanup - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ncbigenomedownload: \$(echo \$(ncbi-genome-download --version 2>&1) | sed 's/ncbi-genome-download //') - END_VERSIONS - """ -} diff --git a/modules/ncbigenomedownload/module.config b/modules/ncbigenomedownload/module.config deleted file mode 100644 index b793c6e5b..000000000 --- a/modules/ncbigenomedownload/module.config +++ /dev/null @@ -1,47 +0,0 @@ -// bactopia-lint: ignore MC009,JS004 -params { - // ncbigenomedownload - accession = null - accessions = null - assembly_level = "complete" - format = "fasta" - keep_downloads = false - kingdom = "bacteria" - limit = null - max_retry = 10 - section = "refseq" - species = null -} - -process { - withName: 'NCBIGENOMEDOWNLOAD' { - ext.wf = params.wf - ext.scope = "run" - ext.subdir = "" - ext.logs_subdir = "" - ext.process_name = "ncbigenomedownload" - - // Tool arguments - ext.args = [ - params.kingdom, - "--section ${params.section}", - "--formats ${params.format}", - "--assembly-levels ${params.assembly_level}", - "--verbose", - params.enable_conda ? "" : "--no-cache" - ].join(' ').replaceAll("\\s{2,}", " ").trim() - - // Environment information - ext.toolName = "bioconda::ncbi-genome-download=0.3.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/ncbi-genome-download:0.3.3--pyh7cba7a3_0" - ext.image = "https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.3--pyh7cba7a3_0" - ext.condaDir = "${params.condadir}" - - // Module-specific parameters - ext.max_retry = params.max_retry - ext.meta_id = "ncbigenomedownload" - ext.meta_limit = params.limit - ext.meta_accession = params.accession - ext.meta_species = params.species - } -} diff --git a/modules/ncbigenomedownload/schema.json b/modules/ncbigenomedownload/schema.json deleted file mode 100644 index 92becdc63..000000000 --- a/modules/ncbigenomedownload/schema.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/ncbigenomedownload/schema.json", - "title": "NCBI Genome Download Module", - "description": "A module to download assemblies from NCBI's Assembly database", - "type": "object", - "$defs": { - "ncbigenomedownload_parameters": { - "title": "NCBI Genome Download Parameters", - "type": "object", - "description": "", - "default": "", - "fa_icon": "fas fa-exclamation-circle", - "properties": { - "species": { - "type": "string", - "description": "Name of the species to download assemblies", - "fa_icon": "fas fa-font" - }, - "accession": { - "type": "string", - "description": "An NCBI Assembly accession to be downloaded", - "fa_icon": "fas fa-font" - }, - "accessions": { - "type": "string", - "description": "An file of NCBI Assembly accessions (one per line) to be downloaded", - "fa_icon": "fas fa-font" - }, - "format": { - "type": "string", - "default": "fasta", - "description": "Comma separated list of formats to download", - "fa_icon": "fas fa-font" - }, - "section": { - "type": "string", - "default": "refseq", - "description": "NCBI section to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "assembly_level": { - "type": "string", - "default": "complete", - "description": "Comma separated list of assembly levels to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "kingdom": { - "type": "string", - "default": "bacteria", - "description": "Comma separated list of formats to download", - "fa_icon": "fas fa-font", - "hidden": true - }, - "limit": { - "type": "string", - "description": "Limit the number of assemblies to download", - "help": "If the the number of available genomes exceeds the given limit, a random subset will be selected.", - "fa_icon": "fas fa-font" - }, - "keep_downloads": { - "type": "boolean", - "default": false, - "description": "Save downloaded files into the bactopia-runs folder", - "fa_icon": "fas fa-toggle-on" - } - } - } - }, - "allOf": [ - { - "$ref": "#/$defs/ncbigenomedownload_parameters" - } - ] -} diff --git a/modules/ncbigenomedownload/tests/main.nf.test b/modules/ncbigenomedownload/tests/main.nf.test deleted file mode 100644 index 06aba434c..000000000 --- a/modules/ncbigenomedownload/tests/main.nf.test +++ /dev/null @@ -1,36 +0,0 @@ -nextflow_process { - name "Test NCBIGENOMEDOWNLOAD" - script "../main.nf" - process "NCBIGENOMEDOWNLOAD" - tag "modules" - tag "ncbigenomedownload" - - test("ncbigenomedownload - module - single accession") { - - when { - params { - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - // Use a small genome for fast testing - accession = "GCF_000292685.1" - format = "fasta" - keep_downloads = true - } - process { - """ - input[0] = null - """ - } - } - - then { - def record = process.out[0][0] - assertAll( - { assert process.success }, - { assert snapshot( - record.meta, - record.versions - ).match() } - ) - } - } -} diff --git a/modules/ncbigenomedownload/tests/main.nf.test.snap b/modules/ncbigenomedownload/tests/main.nf.test.snap deleted file mode 100644 index da429f21d..000000000 --- a/modules/ncbigenomedownload/tests/main.nf.test.snap +++ /dev/null @@ -1,25 +0,0 @@ -{ - "ncbigenomedownload - module - single accession": { - "content": [ - { - "accession": "GCF_000292685.1", - "id": "ncbigenomedownload", - "limit": null, - "logs_dir": "ncbigenomedownload/logs", - "name": "ncbigenomedownload", - "output_dir": "ncbigenomedownload", - "process_name": "ncbigenomedownload", - "scope": "run", - "species": null - }, - [ - "versions.yml:md5,d7681d23ac421c72e51b4b078d708abb" - ] - ], - "timestamp": "2026-04-29T11:15:52.438541392", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - } -} \ No newline at end of file diff --git a/modules/ncbigenomedownload/tests/nextflow.config b/modules/ncbigenomedownload/tests/nextflow.config deleted file mode 100644 index dcba99ffd..000000000 --- a/modules/ncbigenomedownload/tests/nextflow.config +++ /dev/null @@ -1,39 +0,0 @@ -// Minimal config for module-level testing of NCBIGENOMEDOWNLOAD -nextflow.enable.types = true -nextflow.enable.strict = true - -params { - workflow { - name = "ncbigenomedownload" - logo_name = "bactopia-tools" - description = "Download assemblies and annotation files from NCBI's Assembly database" - ext = "fna" - } - - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" - wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - - // ncbi-genome-download uses enable_conda in module.config - enable_conda = false -} - -includeConfig "../module.config" -includeConfig "../../../conf/base.config" -includeConfig "../../../conf/profiles.config" diff --git a/modules/ncbigenomedownload/tests/nf-test.config b/modules/ncbigenomedownload/tests/nf-test.config deleted file mode 100644 index 1f765f697..000000000 --- a/modules/ncbigenomedownload/tests/nf-test.config +++ /dev/null @@ -1,11 +0,0 @@ -config { - testsDir "." - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" - configFile "nextflow.config" - profile "docker" - options "--is_ci --max_memory 8.GB" - - plugins { - load "nft-utils@0.0.5" - } -} diff --git a/subworkflows/bactopia/gather/main.nf b/subworkflows/bactopia/gather/main.nf index f08005c64..8c61b6798 100644 --- a/subworkflows/bactopia/gather/main.nf +++ b/subworkflows/bactopia/gather/main.nf @@ -13,7 +13,7 @@ * @status stable * @keywords validation, download, merging, simulation, metadata, fastq, sra, ena, art * @tags complexity:complex input-type:single output-type:multiple features:aggregation,resource-download,conditional-logic,no-test - * @citation art, fastq_dl, fastq_scan, ncbigenomedownload, pigz + * @citation art, fastq_dl, fastq_scan, genome_dl, pigz * * @modules bactopia_gather, csvtk_concat * diff --git a/subworkflows/ncbigenomedownload/main.nf b/subworkflows/ncbigenomedownload/main.nf deleted file mode 100644 index 880ba1f4b..000000000 --- a/subworkflows/ncbigenomedownload/main.nf +++ /dev/null @@ -1,67 +0,0 @@ -/** - * Download bacterial genomes from NCBI's RefSeq database. - * - * This subworkflow downloads complete and draft bacterial genomes using the - * [ncbi-genome-download](https://github.com/kblin/ncbi-genome-download) tool. It fetches - * genome assemblies in various formats including GenBank, GFF, and FASTA files - * along with associated annotation files and statistics. - * - * @status stable - * @keywords download, ncbi, refseq, genome, assembly, database - * @tags complexity:moderate input-type:single output-type:multiple features:resource-download,database-dependent - * @citation ncbigenomedownload - * - * @modules ncbigenomedownload as ncbigenomedownload_module - * - * @input accessions - * A file containing NCBI accession numbers, one per line. If empty, will download all genomes matching the specified criteria. - * - * @output sample_outputs - * - `gbff`: GenBank format genome sequences - * - `fna`: Genomic nucleotide sequences in FASTA format - * - `gff`: Genome annotations in GFF3 format - * - `faa`: Protein sequences in FASTA format - * - `gpff`: Protein sequences in GenPept format - * - `wgs_gbk`: WGS master records in GenBank format - * - `cds`: CDS nucleotide sequences in FASTA format - * - `rna`: RNA product sequences in FASTA format - * - `rna_fna`: RNA feature nucleotide sequences in FASTA format - * - `features`: Feature table with locations and attributes - * - `rm`: RepeatMasker output (optional) - * - `report`: Assembly report with unit and sequence relationships - * - `stats`: Assembly statistics - * - `accessions`: Generated accession list files - * @output bactopia_tools Downloaded files formatted for Bactopia Tools workflows - * - * @output run_outputs - * - * @output assemblies - * - `fna`: Individual downloaded assembly in FASTA format - * - * @output reference - * First downloaded assembly file for use as a reference genome - */ -nextflow.enable.types = true - -include { NCBIGENOMEDOWNLOAD as NCBIGENOMEDOWNLOAD_MODULE } from '../../modules/ncbigenomedownload/main' - -workflow NCBIGENOMEDOWNLOAD { - - take: - accessions: Path? - - main: - ch_ncbigenomedownload = NCBIGENOMEDOWNLOAD_MODULE(accessions) - ch_assemblies = ch_ncbigenomedownload.map { r -> r.results }.flatten().map { path -> - record(meta: record(id: file(path).getSimpleName()), fna: path) - } - ch_reference = ch_ncbigenomedownload.map { r -> r.results }.flatten().first() - - emit: // bactopia-lint: ignore S005, S010 - // Downstream inputs - assemblies = ch_assemblies - reference = ch_reference - // Published outputs - sample_outputs = ch_ncbigenomedownload - run_outputs = channel.empty() -} diff --git a/subworkflows/ncbigenomedownload/tests/.nftignore b/subworkflows/ncbigenomedownload/tests/.nftignore deleted file mode 100644 index 7b276dee3..000000000 --- a/subworkflows/ncbigenomedownload/tests/.nftignore +++ /dev/null @@ -1,2 +0,0 @@ -**/*.{err,log,stderr,stdout} -**/*.command.* diff --git a/subworkflows/ncbigenomedownload/tests/main.nf.test b/subworkflows/ncbigenomedownload/tests/main.nf.test deleted file mode 100644 index 4d168632e..000000000 --- a/subworkflows/ncbigenomedownload/tests/main.nf.test +++ /dev/null @@ -1,35 +0,0 @@ -nextflow_workflow { - name "Test NCBIGENOMEDOWNLOAD Subworkflow" - script "../main.nf" - workflow "NCBIGENOMEDOWNLOAD" - tag "subworkflows" - tag "ncbigenomedownload" - - test("ncbigenomedownload - subworkflow - single accession") { - when { - params { - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - // Use a small genome for fast testing (requires internet access) - accession = "GCF_000292685.1" - format = "fasta" - keep_downloads = true - } - workflow { - """ - input[0] = null - """ - } - } - - then { - def sample = workflow.out.sample_outputs[0] - assertAll( - { assert workflow.success }, - { assert snapshot( - sample.meta, - sample.versions - ).match() } - ) - } - } -} diff --git a/subworkflows/ncbigenomedownload/tests/main.nf.test.snap b/subworkflows/ncbigenomedownload/tests/main.nf.test.snap deleted file mode 100644 index 67bc3b80c..000000000 --- a/subworkflows/ncbigenomedownload/tests/main.nf.test.snap +++ /dev/null @@ -1,25 +0,0 @@ -{ - "ncbigenomedownload - subworkflow - single accession": { - "content": [ - { - "accession": "GCF_000292685.1", - "id": "ncbigenomedownload", - "limit": null, - "logs_dir": "ncbigenomedownload/logs", - "name": "ncbigenomedownload", - "output_dir": "ncbigenomedownload", - "process_name": "ncbigenomedownload", - "scope": "run", - "species": null - }, - [ - "versions.yml:md5,6ecc191283714fbb0fbc752c9911bf44" - ] - ], - "timestamp": "2026-04-29T11:19:37.454604971", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - } -} \ No newline at end of file diff --git a/subworkflows/ncbigenomedownload/tests/nextflow.config b/subworkflows/ncbigenomedownload/tests/nextflow.config deleted file mode 100644 index 9ae560ede..000000000 --- a/subworkflows/ncbigenomedownload/tests/nextflow.config +++ /dev/null @@ -1,39 +0,0 @@ -// Minimal config for subworkflow-level testing of NCBIGENOMEDOWNLOAD -nextflow.enable.types = true -nextflow.enable.strict = true - -params { - workflow { - name = "ncbigenomedownload" - logo_name = "bactopia-tools" - description = "Download genomes from NCBI" - ext = "fna" - } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" - wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" -} - -// Load module configs for processes in this subworkflow -includeConfig "../../../modules/ncbigenomedownload/module.config" - -// Base config (container resolution + resource labels) -includeConfig "../../../conf/base.config" -includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ncbigenomedownload/tests/nf-test.config b/subworkflows/ncbigenomedownload/tests/nf-test.config deleted file mode 100644 index 1f765f697..000000000 --- a/subworkflows/ncbigenomedownload/tests/nf-test.config +++ /dev/null @@ -1,11 +0,0 @@ -config { - testsDir "." - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" - configFile "nextflow.config" - profile "docker" - options "--is_ci --max_memory 8.GB" - - plugins { - load "nft-utils@0.0.5" - } -} From 113190dcb5bbe3dea52020610193072164d63da5 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 15:32:37 -0600 Subject: [PATCH 22/43] add --fastani_pairwise for explicit pairwise tests, updated docs to be tter reflect this behavior --- CHANGELOG.md | 6 +++++- modules/fastani/module.config | 2 +- modules/fastani/schema.json | 4 ++-- workflows/bactopia-tools/fastani/main.nf | 9 ++++++++- workflows/bactopia-tools/fastani/nextflow_schema.json | 4 ++-- 5 files changed, 18 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a57702d75..b7994b7ce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ sidebar_position: 5000 # Changelog -## v4.0.1 bactopia/bactopia "???" 2026/??/?? +## v4.1.0 bactopia/bactopia "???" 2026/??/?? ### `Added` @@ -52,6 +52,10 @@ sidebar_position: 5000 bundled protein set; every other run failed with `Input file './data/proteins.faa' does not exist`. The default is now anchored on the new `params.bactopia_dir` and resolves to `data/proteins.faa` from any working directory +- `fastani` documenting a `--fastani_skip_pairwise` parameter that does not exist. The parameter + the workflow actually reads is `--fastani_pairwise`, so neither `--help` nor the docs site + mentioned the only way to run FastANI without `--fastani_reference`, `--accession`, + `--accessions`, or `--species`. The requirement is now stated in the `fastani` GroovyDoc ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/modules/fastani/module.config b/modules/fastani/module.config index 450ebb1d5..2e535e52c 100644 --- a/modules/fastani/module.config +++ b/modules/fastani/module.config @@ -3,8 +3,8 @@ params { fastani_frag_len = 3000 fastani_kmer = 16 fastani_min_fraction = 0.2 + fastani_pairwise = false fastani_reference = null - fastani_skip_pairwise = false } process { diff --git a/modules/fastani/schema.json b/modules/fastani/schema.json index 60452ad54..5e4db8e3c 100644 --- a/modules/fastani/schema.json +++ b/modules/fastani/schema.json @@ -37,10 +37,10 @@ "description": "fragment length", "fa_icon": "fas fa-hashtag" }, - "fastani_skip_pairwise": { + "fastani_pairwise": { "type": "boolean", "default": false, - "description": "Only use RefSeq or local assemblies for ANI calculations", + "description": "Add every sample to the reference set, comparing each sample against every other sample in addition to any other references", "fa_icon": "fas fa-toggle-on" } } diff --git a/workflows/bactopia-tools/fastani/main.nf b/workflows/bactopia-tools/fastani/main.nf index d44629679..be5749788 100644 --- a/workflows/bactopia-tools/fastani/main.nf +++ b/workflows/bactopia-tools/fastani/main.nf @@ -6,6 +6,13 @@ * nucleotide identity (ANI) between samples. It can also calculate ANI against reference genomes * by downloading NCBI assemblies using genome-dl. * + * If you do not provide `--fastani_pairwise` then you must provide at least one: + * + * - `--fastani_reference` a local FASTA file to use as a reference for ANI comparison + * - `--accession` a specific NCBI Assembly accession to download + * - `--accessions` a path to a file containing list of NCBI Assembly accessions to download + * - `--species` a species name to download all NCBI genomes for comparison + * * @status stable * @keywords ani, average nucleotide identity, similarity, comparative genomics, bactopia-tool * @tags complexity:moderate input-type:parameter output-type:multiple features:bactopia-tool,comparative @@ -20,7 +27,7 @@ * Path to reference FASTA file for ANI comparison * * @input fastani_pairwise - * Perform pairwise ANI calculation between all samples + * Add every sample to the reference set, comparing each sample against every other sample * * @input species * Species name to download all NCBI genomes for comparison diff --git a/workflows/bactopia-tools/fastani/nextflow_schema.json b/workflows/bactopia-tools/fastani/nextflow_schema.json index e51a921a7..ce194b890 100644 --- a/workflows/bactopia-tools/fastani/nextflow_schema.json +++ b/workflows/bactopia-tools/fastani/nextflow_schema.json @@ -74,10 +74,10 @@ "description": "fragment length", "fa_icon": "fas fa-hashtag" }, - "fastani_skip_pairwise": { + "fastani_pairwise": { "type": "boolean", "default": false, - "description": "Only use RefSeq or local assemblies for ANI calculations", + "description": "Add every sample to the reference set, comparing each sample against every other sample in addition to any other references", "fa_icon": "fas fa-toggle-on" } } From 029c207539787c6ca211178b8f77153a06bc80d1 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 16:18:42 -0600 Subject: [PATCH 23/43] fix mlst workflow not falling back on database downloaded fromdatasets --- CHANGELOG.md | 8 ++++++++ catalog.json | 5 +++-- modules/amrfinderplus/run/module.config | 2 +- modules/amrfinderplus/run/schema.json | 1 - modules/mlst/module.config | 2 +- modules/mlst/schema.json | 1 - nextflow_schema.json | 2 -- .../amrfinderplus/nextflow_schema.json | 1 - workflows/bactopia-tools/mlst/main.nf | 14 +++++++++++--- workflows/bactopia-tools/mlst/nextflow.config | 1 + workflows/bactopia-tools/mlst/nextflow_schema.json | 1 - workflows/staphopia/nextflow_schema.json | 2 -- 12 files changed, 25 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7994b7ce..95b982625 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -56,6 +56,14 @@ sidebar_position: 5000 the workflow actually reads is `--fastani_pairwise`, so neither `--help` nor the docs site mentioned the only way to run FastANI without `--fastani_reference`, `--accession`, `--accessions`, or `--species`. The requirement is now stated in the `fastani` GroovyDoc +- `mlst` and `amrfinderplus` Bactopia Tools failing immediately with `ERROR ~ Path string cannot + be empty` when run without `--mlst_db` / `--amrfinderplus_db` ([#673](https://github.com/bactopia/bactopia/issues/673)). + Both params defaulted to `""`, and Nextflow's static typing coerces the default to a `Path` at + parameter declaration, before the workflow body runs, so `amrfinderplus`'s existing + `if (params.amrfinderplus_db)` fallback was unreachable. Both now default to `null` +- `mlst` Bactopia Tool having no way to source the PubMLST database automatically. It passed + `params.mlst_db` straight through, so `--mlst_db` was effectively required. It now falls back to + the `bactopia_datasets` subworkflow, matching `amrfinderplus` ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/catalog.json b/catalog.json index c8e8c8aea..d4d29634c 100644 --- a/catalog.json +++ b/catalog.json @@ -1,6 +1,6 @@ { "version": "1.0", - "generated": "2026-07-27T20:46:58Z", + "generated": "2026-07-27T21:57:49Z", "bactopia_version": "4.0.1", "bactopia_py_version": "2.2.0", "nf_bactopia_version": "2.1.6", @@ -6939,7 +6939,8 @@ "fna" ], "subworkflows": [ - "mlst" + "mlst", + "bactopia_datasets" ] }, "mobsuite": { diff --git a/modules/amrfinderplus/run/module.config b/modules/amrfinderplus/run/module.config index 4e7875bc2..bc8923cb4 100644 --- a/modules/amrfinderplus/run/module.config +++ b/modules/amrfinderplus/run/module.config @@ -2,7 +2,7 @@ params { // amrfinderplus_run amrfinderplus_coverage_min = 0.5 - amrfinderplus_db = "" + amrfinderplus_db = null amrfinderplus_ident_min = -1 amrfinderplus_noplus = false amrfinderplus_opts = "" diff --git a/modules/amrfinderplus/run/schema.json b/modules/amrfinderplus/run/schema.json index 2c58043f6..06ad4e07f 100644 --- a/modules/amrfinderplus/run/schema.json +++ b/modules/amrfinderplus/run/schema.json @@ -67,7 +67,6 @@ }, "amrfinderplus_db": { "type": "string", - "default": "", "description": "A custom AMRFinder+ database to use, either a tarball or a folder", "fa_icon": "fas fa-font", "hidden": true diff --git a/modules/mlst/module.config b/modules/mlst/module.config index df1efab7b..c613b3609 100644 --- a/modules/mlst/module.config +++ b/modules/mlst/module.config @@ -1,6 +1,6 @@ params { // mlst - mlst_db = "" + mlst_db = null mlst_mincov = 10 mlst_minid = 95 mlst_minscore = 50 diff --git a/modules/mlst/schema.json b/modules/mlst/schema.json index b31c04477..70ec9639a 100644 --- a/modules/mlst/schema.json +++ b/modules/mlst/schema.json @@ -44,7 +44,6 @@ }, "mlst_db": { "type": "string", - "default": "", "description": "A custom MLST database to use, either a tarball or a directory", "fa_icon": "fas fa-font" } diff --git a/nextflow_schema.json b/nextflow_schema.json index 8bdd973c6..f9dc9517b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -188,7 +188,6 @@ }, "amrfinderplus_db": { "type": "string", - "default": "", "description": "A custom AMRFinder+ database to use, either a tarball or a folder", "fa_icon": "fas fa-font", "hidden": true @@ -564,7 +563,6 @@ }, "mlst_db": { "type": "string", - "default": "", "description": "A custom MLST database to use, either a tarball or a directory", "fa_icon": "fas fa-font", "hidden": true diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json b/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json index 411823d37..2dc78507b 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json +++ b/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json @@ -104,7 +104,6 @@ }, "amrfinderplus_db": { "type": "string", - "default": "", "description": "A custom AMRFinder+ database to use, either a tarball or a folder", "fa_icon": "fas fa-font", "hidden": true diff --git a/workflows/bactopia-tools/mlst/main.nf b/workflows/bactopia-tools/mlst/main.nf index 4448e19fb..7773e83e8 100644 --- a/workflows/bactopia-tools/mlst/main.nf +++ b/workflows/bactopia-tools/mlst/main.nf @@ -12,13 +12,14 @@ * @tags complexity:simple input-type:parameter output-type:multiple features:bactopia-tool,aggregation * @citation csvtk, mlst, pubmlst * - * @subworkflows utils_bactopia-tools, mlst + * @subworkflows utils_bactopia-tools, mlst, bactopia_datasets * * @input rundir * Directory containing results from a completed Bactopia analysis run * * @input mlst_db - * Path to a pre-built MLST database directory (optional — auto-detected otherwise) + * Path to a custom MLST database, either a tarball or a directory. When omitted, the + * database is sourced from the Bactopia datasets. * * @section Per-Sample Results * @publish *.tsv Tab-delimited file with MLST results including scheme, ST, and allele profiles @@ -44,12 +45,19 @@ params { include { BACTOPIATOOL_INIT } from '../../../subworkflows/utils/bactopia-tools/main' include { MLST } from '../../../subworkflows/mlst/main' +include { DATASETS } from '../../../subworkflows/bactopia/datasets/main' include { collectNextflowLogs } from 'plugin/nf-bactopia' workflow { main: ch_bactopiatool = BACTOPIATOOL_INIT() - ch_mlst = MLST(ch_bactopiatool.assembly, params.mlst_db) + + if (params.mlst_db) { + ch_mlst = MLST(ch_bactopiatool.assembly, params.mlst_db) + } else { + ch_datasets = DATASETS() + ch_mlst = MLST(ch_bactopiatool.assembly, ch_datasets.mlst_db) + } publish: // Per-sample diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index a1cd2b7ff..3792ff1fc 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -33,6 +33,7 @@ includeConfig "../../../conf/params/bactopia-tools.config" // Module specific config includeConfig "../../../modules/csvtk/concat/module.config" includeConfig "../../../modules/mlst/module.config" +includeConfig "../../../modules/bactopia/datasets/module.config" // Set output directory outputDir = params.outdir diff --git a/workflows/bactopia-tools/mlst/nextflow_schema.json b/workflows/bactopia-tools/mlst/nextflow_schema.json index 9876f9ee1..51dbb464e 100644 --- a/workflows/bactopia-tools/mlst/nextflow_schema.json +++ b/workflows/bactopia-tools/mlst/nextflow_schema.json @@ -81,7 +81,6 @@ }, "mlst_db": { "type": "string", - "default": "", "description": "A custom MLST database to use, either a tarball or a directory", "fa_icon": "fas fa-font" } diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index 76cfce481..9bf28d0bd 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -183,7 +183,6 @@ }, "amrfinderplus_db": { "type": "string", - "default": "", "description": "A custom AMRFinder+ database to use, either a tarball or a folder", "fa_icon": "fas fa-font", "hidden": true @@ -559,7 +558,6 @@ }, "mlst_db": { "type": "string", - "default": "", "description": "A custom MLST database to use, either a tarball or a directory", "fa_icon": "fas fa-font", "hidden": true From fbf1adca7f4bb367530e2686142010cf8a71e4b4 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 17:04:04 -0600 Subject: [PATCH 24/43] fix mobsuite bug when input had no plasmids (tried to compress non-existent fasta file) --- CHANGELOG.md | 5 +++ modules/mobsuite/recon/main.nf | 4 +-- modules/mobsuite/recon/tests/main.nf.test | 32 +++++++++++++++++++ .../mobsuite/recon/tests/main.nf.test.snap | 25 +++++++++++++++ 4 files changed, 64 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95b982625..f6f2f8fa6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,11 @@ sidebar_position: 5000 - `mlst` Bactopia Tool having no way to source the PubMLST database automatically. It passed `params.mlst_db` straight through, so `--mlst_db` was effectively required. It now falls back to the `bactopia_datasets` subworkflow, matching `amrfinderplus` +- `mobsuite` failing on any sample with no reconstructed plasmids. After `chromosome.fasta` was + moved out of `supplemental/`, the cleanup step ran `gzip supplemental/*.fasta` on an unguarded + glob; with no plasmids nothing matched, `gzip` exited non-zero, and Nextflow's `bash -ue` + aborted the task even though `mob_recon` had succeeded. Cleanup now uses `find -exec`, which + is a no-op when there is nothing to compress ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/modules/mobsuite/recon/main.nf b/modules/mobsuite/recon/main.nf index 60b81b466..8c13ec382 100644 --- a/modules/mobsuite/recon/main.nf +++ b/modules/mobsuite/recon/main.nf @@ -97,8 +97,8 @@ process MOBSUITE_RECON { fi # Cleanup - gzip supplemental/*.fasta - mv supplemental/*.fasta.gz ./ + find supplemental/ -maxdepth 1 -name "*.fasta" -exec gzip {} \\; + find supplemental/ -maxdepth 1 -name "*.fasta.gz" -exec mv {} ./ \\; if [ "${is_compressed}" == "true" ]; then rm -rf ${fasta_name} fi diff --git a/modules/mobsuite/recon/tests/main.nf.test b/modules/mobsuite/recon/tests/main.nf.test index 603f56a0b..8edf6cbdf 100644 --- a/modules/mobsuite/recon/tests/main.nf.test +++ b/modules/mobsuite/recon/tests/main.nf.test @@ -67,4 +67,36 @@ nextflow_process { ) } } + + test("mobsuite_recon - module - GCF_006364235 - no plasmids") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_006364235"], + fna: file("${params.test_data_dir}/species/streptococcus_pyogenes/uncompressed/GCF_006364235/main/assembler/GCF_006364235.fna") + ) + ) + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.chromosome, + record.contig_report, + record.plasmids, + record.versions + ).match() } + ) + } + } } diff --git a/modules/mobsuite/recon/tests/main.nf.test.snap b/modules/mobsuite/recon/tests/main.nf.test.snap index c77bf0f41..f551a776e 100644 --- a/modules/mobsuite/recon/tests/main.nf.test.snap +++ b/modules/mobsuite/recon/tests/main.nf.test.snap @@ -1,4 +1,29 @@ { + "mobsuite_recon - module - GCF_006364235 - no plasmids": { + "content": [ + { + "id": "GCF_006364235-MOBSUITE_RECON", + "logs_dir": "GCF_006364235/tools/mobsuite//logs/", + "name": "GCF_006364235", + "output_dir": "GCF_006364235/tools/mobsuite/", + "process_name": "mobsuite", + "scope": "sample" + }, + "GCF_006364235-chromosome.fasta.gz:md5,6a71b83161328f8b0d8df42f1d30e853", + "GCF_006364235-contig_report.txt:md5,8aa74842a7a0af81d899b4d64f5f7c5b", + [ + + ], + [ + "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" + ] + ], + "timestamp": "2026-07-27T16:45:56.17998057", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } + }, "mobsuite_recon - module - GCF_000017085 - compressed": { "content": [ { From c3210ad44388fd677a5cd358635b4e0f3578e096 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 27 Jul 2026 18:31:45 -0600 Subject: [PATCH 25/43] fix stecfinder trying to import non-existent reads and failing silently --- conf/params.config | 1 - conf/schema/generic.json | 7 ---- nextflow_schema.json | 7 ---- subworkflows/stecfinder/main.nf | 8 +++- subworkflows/stecfinder/tests/main.nf.test | 39 +++++++++++++++++++ .../abricate/nextflow_schema.json | 7 ---- .../abritamr/nextflow_schema.json | 7 ---- .../agrvate/nextflow_schema.json | 7 ---- .../amrfinderplus/nextflow_schema.json | 7 ---- .../bactopia-tools/ariba/nextflow_schema.json | 7 ---- .../bactopia-tools/bakta/nextflow_schema.json | 7 ---- .../blastn/nextflow_schema.json | 7 ---- .../blastp/nextflow_schema.json | 7 ---- .../blastx/nextflow_schema.json | 7 ---- .../bracken/nextflow_schema.json | 7 ---- .../btyper3/nextflow_schema.json | 7 ---- .../bactopia-tools/busco/nextflow_schema.json | 7 ---- .../checkm/nextflow_schema.json | 7 ---- .../checkm2/nextflow_schema.json | 7 ---- .../clermontyping/nextflow_schema.json | 7 ---- .../defensefinder/nextflow_schema.json | 7 ---- .../ectyper/nextflow_schema.json | 7 ---- .../eggnog/nextflow_schema.json | 7 ---- .../emmtyper/nextflow_schema.json | 7 ---- .../fastani/nextflow_schema.json | 7 ---- .../bactopia-tools/gamma/nextflow_schema.json | 7 ---- .../genotyphi/nextflow_schema.json | 7 ---- .../gigatyper/nextflow_schema.json | 7 ---- .../bactopia-tools/gtdb/nextflow_schema.json | 7 ---- .../bactopia-tools/hicap/nextflow_schema.json | 7 ---- .../hpsuissero/nextflow_schema.json | 7 ---- .../ismapper/nextflow_schema.json | 7 ---- .../kleborate/nextflow_schema.json | 7 ---- .../kraken2/nextflow_schema.json | 7 ---- .../legsta/nextflow_schema.json | 7 ---- .../lissero/nextflow_schema.json | 7 ---- .../mashdist/nextflow_schema.json | 7 ---- .../mashtree/nextflow_schema.json | 7 ---- .../mcroni/nextflow_schema.json | 7 ---- .../meningotype/nextflow_schema.json | 7 ---- .../merlin/nextflow_schema.json | 7 ---- .../bactopia-tools/midas/nextflow_schema.json | 7 ---- .../bactopia-tools/mlst/nextflow_schema.json | 7 ---- .../mobsuite/nextflow_schema.json | 7 ---- .../mykrobe/nextflow_schema.json | 7 ---- .../ngmaster/nextflow_schema.json | 7 ---- .../pangenome/nextflow_schema.json | 7 ---- .../bactopia-tools/pasty/nextflow_schema.json | 7 ---- .../pbptyper/nextflow_schema.json | 7 ---- .../phispy/nextflow_schema.json | 7 ---- .../plasmidfinder/nextflow_schema.json | 7 ---- .../pneumocat/nextflow_schema.json | 7 ---- .../prokka/nextflow_schema.json | 7 ---- .../bactopia-tools/quast/nextflow_schema.json | 7 ---- .../bactopia-tools/rgi/nextflow_schema.json | 7 ---- .../sccmec/nextflow_schema.json | 7 ---- .../scrubber/nextflow_schema.json | 7 ---- .../seqsero2/nextflow_schema.json | 7 ---- .../seroba/nextflow_schema.json | 7 ---- .../shigapass/nextflow_schema.json | 7 ---- .../shigatyper/nextflow_schema.json | 7 ---- .../shigeifinder/nextflow_schema.json | 7 ---- .../bactopia-tools/sistr/nextflow_schema.json | 7 ---- .../snippy/nextflow_schema.json | 7 ---- .../spatyper/nextflow_schema.json | 7 ---- .../ssuissero/nextflow_schema.json | 7 ---- .../staphscan/nextflow_schema.json | 7 ---- .../staphtyper/nextflow_schema.json | 7 ---- .../stecfinder/nextflow_schema.json | 7 ---- .../stxtyper/nextflow_schema.json | 7 ---- .../bactopia-tools/sylph/nextflow_schema.json | 7 ---- .../tblastn/nextflow_schema.json | 7 ---- .../tblastx/nextflow_schema.json | 7 ---- .../tbprofiler/nextflow_schema.json | 7 ---- .../traitar/nextflow_schema.json | 7 ---- workflows/cleanyerreads/nextflow_schema.json | 7 ---- workflows/staphopia/nextflow_schema.json | 7 ---- workflows/teton/nextflow_schema.json | 7 ---- 78 files changed, 46 insertions(+), 527 deletions(-) diff --git a/conf/params.config b/conf/params.config index e002f4707..8f48dbefe 100644 --- a/conf/params.config +++ b/conf/params.config @@ -38,7 +38,6 @@ params { help = null help_all = false sleep_time = 5 - validate_params = true //nf-core monochrome_logs = false diff --git a/conf/schema/generic.json b/conf/schema/generic.json index 89bde2c7c..b9044ebc3 100644 --- a/conf/schema/generic.json +++ b/conf/schema/generic.json @@ -303,13 +303,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/nextflow_schema.json b/nextflow_schema.json index f9dc9517b..8a3e48c6b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2284,13 +2284,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/subworkflows/stecfinder/main.nf b/subworkflows/stecfinder/main.nf index e893afd5b..ad315601f 100644 --- a/subworkflows/stecfinder/main.nf +++ b/subworkflows/stecfinder/main.nf @@ -38,7 +38,13 @@ workflow STECFINDER { seqs: Channel main: - ch_stecfinder = STECFINDER_MODULE(seqs) + // If user passes --stecfinder_use_reads, we have to filter out any samples that + // have no reads. + def ch_seqs = (params.stecfinder_use_reads + ? seqs.filter { r -> [r.r1, r.r2, r.se, r.lr].any { seq -> seq != null } } + : seqs + ).map { r -> record(meta: r.meta, fna: r.fna, r1: r.r1, r2: r.r2, se: r.se, lr: r.lr) } + ch_stecfinder = STECFINDER_MODULE(ch_seqs) ch_csvtk_concat = CSVTK_CONCAT(gatherCsvtk(ch_stecfinder, 'tsv', [name: 'stecfinder']), 'tsv', 'tsv') emit: diff --git a/subworkflows/stecfinder/tests/main.nf.test b/subworkflows/stecfinder/tests/main.nf.test index d28972ccb..988367576 100644 --- a/subworkflows/stecfinder/tests/main.nf.test +++ b/subworkflows/stecfinder/tests/main.nf.test @@ -46,4 +46,43 @@ nextflow_workflow { ) } } + + test("stecfinder - subworkflow - reads mode drops read-less samples") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + stecfinder_use_reads = true + } + workflow { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_002949675"], + fna: file("${params.test_data_dir}/species/shigella_dysenteriae/assembly/GCF_002949675/main/assembler/GCF_002949675.fna.gz"), + r1: file("${params.test_data_dir}/species/shigella_dysenteriae/reads/ERR6005894/main/qc/ERR6005894_R1.fastq.gz"), + r2: file("${params.test_data_dir}/species/shigella_dysenteriae/reads/ERR6005894/main/qc/ERR6005894_R2.fastq.gz"), + se: null, + lr: null + ), + record( + meta: [name: "NOREADS"], + fna: file("${params.test_data_dir}/species/shigella_dysenteriae/assembly/GCF_002949675/main/assembler/GCF_002949675.fna.gz"), + r1: null, + r2: null, + se: null, + lr: null + ) + ) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.out.sample_outputs.size() == 1 }, + { assert workflow.out.sample_outputs[0].meta.name == "GCF_002949675" } + ) + } + } } diff --git a/workflows/bactopia-tools/abricate/nextflow_schema.json b/workflows/bactopia-tools/abricate/nextflow_schema.json index 0bcf5b52a..4e9b9570c 100644 --- a/workflows/bactopia-tools/abricate/nextflow_schema.json +++ b/workflows/bactopia-tools/abricate/nextflow_schema.json @@ -367,13 +367,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/abritamr/nextflow_schema.json b/workflows/bactopia-tools/abritamr/nextflow_schema.json index cd36c99c1..53e30292b 100644 --- a/workflows/bactopia-tools/abritamr/nextflow_schema.json +++ b/workflows/bactopia-tools/abritamr/nextflow_schema.json @@ -375,13 +375,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/agrvate/nextflow_schema.json b/workflows/bactopia-tools/agrvate/nextflow_schema.json index e8c7e8803..24611862d 100644 --- a/workflows/bactopia-tools/agrvate/nextflow_schema.json +++ b/workflows/bactopia-tools/agrvate/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json b/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json index 2dc78507b..1e1713ca0 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json +++ b/workflows/bactopia-tools/amrfinderplus/nextflow_schema.json @@ -424,13 +424,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/ariba/nextflow_schema.json b/workflows/bactopia-tools/ariba/nextflow_schema.json index c0ce0705c..53abce65f 100644 --- a/workflows/bactopia-tools/ariba/nextflow_schema.json +++ b/workflows/bactopia-tools/ariba/nextflow_schema.json @@ -449,13 +449,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/bakta/nextflow_schema.json b/workflows/bactopia-tools/bakta/nextflow_schema.json index 761d16105..f3d9480e2 100644 --- a/workflows/bactopia-tools/bakta/nextflow_schema.json +++ b/workflows/bactopia-tools/bakta/nextflow_schema.json @@ -500,13 +500,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/blastn/nextflow_schema.json b/workflows/bactopia-tools/blastn/nextflow_schema.json index 7dac1817b..ab60faa4f 100644 --- a/workflows/bactopia-tools/blastn/nextflow_schema.json +++ b/workflows/bactopia-tools/blastn/nextflow_schema.json @@ -407,13 +407,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/blastp/nextflow_schema.json b/workflows/bactopia-tools/blastp/nextflow_schema.json index 3b2006eb3..61b841f84 100644 --- a/workflows/bactopia-tools/blastp/nextflow_schema.json +++ b/workflows/bactopia-tools/blastp/nextflow_schema.json @@ -394,13 +394,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/blastx/nextflow_schema.json b/workflows/bactopia-tools/blastx/nextflow_schema.json index f0dc6192b..7072c9625 100644 --- a/workflows/bactopia-tools/blastx/nextflow_schema.json +++ b/workflows/bactopia-tools/blastx/nextflow_schema.json @@ -394,13 +394,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/bracken/nextflow_schema.json b/workflows/bactopia-tools/bracken/nextflow_schema.json index b9dbce839..86c0e698a 100644 --- a/workflows/bactopia-tools/bracken/nextflow_schema.json +++ b/workflows/bactopia-tools/bracken/nextflow_schema.json @@ -480,13 +480,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/btyper3/nextflow_schema.json b/workflows/bactopia-tools/btyper3/nextflow_schema.json index 80f738097..7beaa7596 100644 --- a/workflows/bactopia-tools/btyper3/nextflow_schema.json +++ b/workflows/bactopia-tools/btyper3/nextflow_schema.json @@ -404,13 +404,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/busco/nextflow_schema.json b/workflows/bactopia-tools/busco/nextflow_schema.json index 1488924fa..41f5d5a73 100644 --- a/workflows/bactopia-tools/busco/nextflow_schema.json +++ b/workflows/bactopia-tools/busco/nextflow_schema.json @@ -425,13 +425,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/checkm/nextflow_schema.json b/workflows/bactopia-tools/checkm/nextflow_schema.json index a381efadc..643eba90c 100644 --- a/workflows/bactopia-tools/checkm/nextflow_schema.json +++ b/workflows/bactopia-tools/checkm/nextflow_schema.json @@ -443,13 +443,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/checkm2/nextflow_schema.json b/workflows/bactopia-tools/checkm2/nextflow_schema.json index 1e736d9e4..4c9603405 100644 --- a/workflows/bactopia-tools/checkm2/nextflow_schema.json +++ b/workflows/bactopia-tools/checkm2/nextflow_schema.json @@ -416,13 +416,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/clermontyping/nextflow_schema.json b/workflows/bactopia-tools/clermontyping/nextflow_schema.json index 811b47683..74f1058ab 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow_schema.json +++ b/workflows/bactopia-tools/clermontyping/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/defensefinder/nextflow_schema.json b/workflows/bactopia-tools/defensefinder/nextflow_schema.json index daeb607e3..7da2d41b5 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow_schema.json +++ b/workflows/bactopia-tools/defensefinder/nextflow_schema.json @@ -394,13 +394,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/ectyper/nextflow_schema.json b/workflows/bactopia-tools/ectyper/nextflow_schema.json index 8d937cbfa..6a9a4a3de 100644 --- a/workflows/bactopia-tools/ectyper/nextflow_schema.json +++ b/workflows/bactopia-tools/ectyper/nextflow_schema.json @@ -403,13 +403,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/eggnog/nextflow_schema.json b/workflows/bactopia-tools/eggnog/nextflow_schema.json index e0e594a8c..fdde4cdd5 100644 --- a/workflows/bactopia-tools/eggnog/nextflow_schema.json +++ b/workflows/bactopia-tools/eggnog/nextflow_schema.json @@ -435,13 +435,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/emmtyper/nextflow_schema.json b/workflows/bactopia-tools/emmtyper/nextflow_schema.json index 33f69e132..338b21b85 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow_schema.json +++ b/workflows/bactopia-tools/emmtyper/nextflow_schema.json @@ -441,13 +441,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/fastani/nextflow_schema.json b/workflows/bactopia-tools/fastani/nextflow_schema.json index ce194b890..812a833c1 100644 --- a/workflows/bactopia-tools/fastani/nextflow_schema.json +++ b/workflows/bactopia-tools/fastani/nextflow_schema.json @@ -457,13 +457,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/gamma/nextflow_schema.json b/workflows/bactopia-tools/gamma/nextflow_schema.json index d0c9da3f6..56f0b8659 100644 --- a/workflows/bactopia-tools/gamma/nextflow_schema.json +++ b/workflows/bactopia-tools/gamma/nextflow_schema.json @@ -405,13 +405,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/genotyphi/nextflow_schema.json b/workflows/bactopia-tools/genotyphi/nextflow_schema.json index dc3d977b0..96d00fde6 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow_schema.json +++ b/workflows/bactopia-tools/genotyphi/nextflow_schema.json @@ -463,13 +463,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/gigatyper/nextflow_schema.json b/workflows/bactopia-tools/gigatyper/nextflow_schema.json index 7e58a0bc9..b28b1edb3 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow_schema.json +++ b/workflows/bactopia-tools/gigatyper/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/gtdb/nextflow_schema.json b/workflows/bactopia-tools/gtdb/nextflow_schema.json index f88b16a96..867c1369f 100644 --- a/workflows/bactopia-tools/gtdb/nextflow_schema.json +++ b/workflows/bactopia-tools/gtdb/nextflow_schema.json @@ -438,13 +438,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/hicap/nextflow_schema.json b/workflows/bactopia-tools/hicap/nextflow_schema.json index f5bbeee70..d0c7a5b0b 100644 --- a/workflows/bactopia-tools/hicap/nextflow_schema.json +++ b/workflows/bactopia-tools/hicap/nextflow_schema.json @@ -415,13 +415,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/hpsuissero/nextflow_schema.json b/workflows/bactopia-tools/hpsuissero/nextflow_schema.json index c99287759..0f44a3c61 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow_schema.json +++ b/workflows/bactopia-tools/hpsuissero/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/ismapper/nextflow_schema.json b/workflows/bactopia-tools/ismapper/nextflow_schema.json index bf30899ea..c5cdfb81b 100644 --- a/workflows/bactopia-tools/ismapper/nextflow_schema.json +++ b/workflows/bactopia-tools/ismapper/nextflow_schema.json @@ -424,13 +424,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/kleborate/nextflow_schema.json b/workflows/bactopia-tools/kleborate/nextflow_schema.json index 05e4f10d3..0ce15a1c5 100644 --- a/workflows/bactopia-tools/kleborate/nextflow_schema.json +++ b/workflows/bactopia-tools/kleborate/nextflow_schema.json @@ -383,13 +383,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/kraken2/nextflow_schema.json b/workflows/bactopia-tools/kraken2/nextflow_schema.json index 4234c281c..9f1bf2bbe 100644 --- a/workflows/bactopia-tools/kraken2/nextflow_schema.json +++ b/workflows/bactopia-tools/kraken2/nextflow_schema.json @@ -422,13 +422,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/legsta/nextflow_schema.json b/workflows/bactopia-tools/legsta/nextflow_schema.json index eb674f0ad..fae366ae8 100644 --- a/workflows/bactopia-tools/legsta/nextflow_schema.json +++ b/workflows/bactopia-tools/legsta/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/lissero/nextflow_schema.json b/workflows/bactopia-tools/lissero/nextflow_schema.json index a958be812..6d22146f8 100644 --- a/workflows/bactopia-tools/lissero/nextflow_schema.json +++ b/workflows/bactopia-tools/lissero/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mashdist/nextflow_schema.json b/workflows/bactopia-tools/mashdist/nextflow_schema.json index 00bb940bb..4f7d7c583 100644 --- a/workflows/bactopia-tools/mashdist/nextflow_schema.json +++ b/workflows/bactopia-tools/mashdist/nextflow_schema.json @@ -433,13 +433,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mashtree/nextflow_schema.json b/workflows/bactopia-tools/mashtree/nextflow_schema.json index e04a494cc..8a64ddc9a 100644 --- a/workflows/bactopia-tools/mashtree/nextflow_schema.json +++ b/workflows/bactopia-tools/mashtree/nextflow_schema.json @@ -460,13 +460,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mcroni/nextflow_schema.json b/workflows/bactopia-tools/mcroni/nextflow_schema.json index 4ec32740c..512636277 100644 --- a/workflows/bactopia-tools/mcroni/nextflow_schema.json +++ b/workflows/bactopia-tools/mcroni/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/meningotype/nextflow_schema.json b/workflows/bactopia-tools/meningotype/nextflow_schema.json index 76280e7fa..f8f599e08 100644 --- a/workflows/bactopia-tools/meningotype/nextflow_schema.json +++ b/workflows/bactopia-tools/meningotype/nextflow_schema.json @@ -395,13 +395,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/merlin/nextflow_schema.json b/workflows/bactopia-tools/merlin/nextflow_schema.json index e06262722..194501ced 100644 --- a/workflows/bactopia-tools/merlin/nextflow_schema.json +++ b/workflows/bactopia-tools/merlin/nextflow_schema.json @@ -1233,13 +1233,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/midas/nextflow_schema.json b/workflows/bactopia-tools/midas/nextflow_schema.json index af51dc363..b5c5be5a2 100644 --- a/workflows/bactopia-tools/midas/nextflow_schema.json +++ b/workflows/bactopia-tools/midas/nextflow_schema.json @@ -415,13 +415,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mlst/nextflow_schema.json b/workflows/bactopia-tools/mlst/nextflow_schema.json index 51dbb464e..4b4554b63 100644 --- a/workflows/bactopia-tools/mlst/nextflow_schema.json +++ b/workflows/bactopia-tools/mlst/nextflow_schema.json @@ -400,13 +400,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mobsuite/nextflow_schema.json b/workflows/bactopia-tools/mobsuite/nextflow_schema.json index e6aaced25..7a8e5d08c 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow_schema.json +++ b/workflows/bactopia-tools/mobsuite/nextflow_schema.json @@ -391,13 +391,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/mykrobe/nextflow_schema.json b/workflows/bactopia-tools/mykrobe/nextflow_schema.json index 20ef49f35..5779168f1 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow_schema.json +++ b/workflows/bactopia-tools/mykrobe/nextflow_schema.json @@ -416,13 +416,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/ngmaster/nextflow_schema.json b/workflows/bactopia-tools/ngmaster/nextflow_schema.json index bf2d9b474..4d5b29dcf 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow_schema.json +++ b/workflows/bactopia-tools/ngmaster/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/pangenome/nextflow_schema.json b/workflows/bactopia-tools/pangenome/nextflow_schema.json index a521917fd..8e7ad3563 100644 --- a/workflows/bactopia-tools/pangenome/nextflow_schema.json +++ b/workflows/bactopia-tools/pangenome/nextflow_schema.json @@ -814,13 +814,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/pasty/nextflow_schema.json b/workflows/bactopia-tools/pasty/nextflow_schema.json index 8f92ff227..6a69bb254 100644 --- a/workflows/bactopia-tools/pasty/nextflow_schema.json +++ b/workflows/bactopia-tools/pasty/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/pbptyper/nextflow_schema.json b/workflows/bactopia-tools/pbptyper/nextflow_schema.json index b8261a65f..079542f60 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow_schema.json +++ b/workflows/bactopia-tools/pbptyper/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/phispy/nextflow_schema.json b/workflows/bactopia-tools/phispy/nextflow_schema.json index 1318a4cce..03692a1cf 100644 --- a/workflows/bactopia-tools/phispy/nextflow_schema.json +++ b/workflows/bactopia-tools/phispy/nextflow_schema.json @@ -410,13 +410,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow_schema.json b/workflows/bactopia-tools/plasmidfinder/nextflow_schema.json index 3cea2e3c8..34fca0d57 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow_schema.json +++ b/workflows/bactopia-tools/plasmidfinder/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/pneumocat/nextflow_schema.json b/workflows/bactopia-tools/pneumocat/nextflow_schema.json index 13031fab6..622a8677c 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow_schema.json +++ b/workflows/bactopia-tools/pneumocat/nextflow_schema.json @@ -340,13 +340,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/prokka/nextflow_schema.json b/workflows/bactopia-tools/prokka/nextflow_schema.json index b0ecbba9a..e5b38acbf 100644 --- a/workflows/bactopia-tools/prokka/nextflow_schema.json +++ b/workflows/bactopia-tools/prokka/nextflow_schema.json @@ -401,13 +401,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/quast/nextflow_schema.json b/workflows/bactopia-tools/quast/nextflow_schema.json index 640a2dfb8..bba3276c4 100644 --- a/workflows/bactopia-tools/quast/nextflow_schema.json +++ b/workflows/bactopia-tools/quast/nextflow_schema.json @@ -389,13 +389,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/rgi/nextflow_schema.json b/workflows/bactopia-tools/rgi/nextflow_schema.json index a4ea5d9f2..fe6c717e0 100644 --- a/workflows/bactopia-tools/rgi/nextflow_schema.json +++ b/workflows/bactopia-tools/rgi/nextflow_schema.json @@ -428,13 +428,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/sccmec/nextflow_schema.json b/workflows/bactopia-tools/sccmec/nextflow_schema.json index 7aef3cfec..a08980b55 100644 --- a/workflows/bactopia-tools/sccmec/nextflow_schema.json +++ b/workflows/bactopia-tools/sccmec/nextflow_schema.json @@ -389,13 +389,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/scrubber/nextflow_schema.json b/workflows/bactopia-tools/scrubber/nextflow_schema.json index 0d07bad93..9f1cf8ea5 100644 --- a/workflows/bactopia-tools/scrubber/nextflow_schema.json +++ b/workflows/bactopia-tools/scrubber/nextflow_schema.json @@ -509,13 +509,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/seqsero2/nextflow_schema.json b/workflows/bactopia-tools/seqsero2/nextflow_schema.json index 6310af987..dbbe0b4b0 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow_schema.json +++ b/workflows/bactopia-tools/seqsero2/nextflow_schema.json @@ -396,13 +396,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/seroba/nextflow_schema.json b/workflows/bactopia-tools/seroba/nextflow_schema.json index dd017d2d5..5be8348b6 100644 --- a/workflows/bactopia-tools/seroba/nextflow_schema.json +++ b/workflows/bactopia-tools/seroba/nextflow_schema.json @@ -378,13 +378,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/shigapass/nextflow_schema.json b/workflows/bactopia-tools/shigapass/nextflow_schema.json index e1629c921..c6b35e5e6 100644 --- a/workflows/bactopia-tools/shigapass/nextflow_schema.json +++ b/workflows/bactopia-tools/shigapass/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/shigatyper/nextflow_schema.json b/workflows/bactopia-tools/shigatyper/nextflow_schema.json index 0d3c169f0..da596446a 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow_schema.json +++ b/workflows/bactopia-tools/shigatyper/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/shigeifinder/nextflow_schema.json b/workflows/bactopia-tools/shigeifinder/nextflow_schema.json index 18bd76dac..b0e253753 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow_schema.json +++ b/workflows/bactopia-tools/shigeifinder/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/sistr/nextflow_schema.json b/workflows/bactopia-tools/sistr/nextflow_schema.json index 167dc5d83..2914af582 100644 --- a/workflows/bactopia-tools/sistr/nextflow_schema.json +++ b/workflows/bactopia-tools/sistr/nextflow_schema.json @@ -371,13 +371,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/snippy/nextflow_schema.json b/workflows/bactopia-tools/snippy/nextflow_schema.json index ee9fb3668..7ce37b95f 100644 --- a/workflows/bactopia-tools/snippy/nextflow_schema.json +++ b/workflows/bactopia-tools/snippy/nextflow_schema.json @@ -654,13 +654,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/spatyper/nextflow_schema.json b/workflows/bactopia-tools/spatyper/nextflow_schema.json index 958666d80..94ad88391 100644 --- a/workflows/bactopia-tools/spatyper/nextflow_schema.json +++ b/workflows/bactopia-tools/spatyper/nextflow_schema.json @@ -383,13 +383,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/ssuissero/nextflow_schema.json b/workflows/bactopia-tools/ssuissero/nextflow_schema.json index 94973c26e..aa2f236ee 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow_schema.json +++ b/workflows/bactopia-tools/ssuissero/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/staphscan/nextflow_schema.json b/workflows/bactopia-tools/staphscan/nextflow_schema.json index 330d1748a..066e805e4 100644 --- a/workflows/bactopia-tools/staphscan/nextflow_schema.json +++ b/workflows/bactopia-tools/staphscan/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/staphtyper/nextflow_schema.json b/workflows/bactopia-tools/staphtyper/nextflow_schema.json index ea891890d..838b74c3a 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow_schema.json +++ b/workflows/bactopia-tools/staphtyper/nextflow_schema.json @@ -452,13 +452,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/stecfinder/nextflow_schema.json b/workflows/bactopia-tools/stecfinder/nextflow_schema.json index 24efa0fd7..39871b635 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow_schema.json +++ b/workflows/bactopia-tools/stecfinder/nextflow_schema.json @@ -445,13 +445,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/stxtyper/nextflow_schema.json b/workflows/bactopia-tools/stxtyper/nextflow_schema.json index 47a1f3c4b..718972fb0 100644 --- a/workflows/bactopia-tools/stxtyper/nextflow_schema.json +++ b/workflows/bactopia-tools/stxtyper/nextflow_schema.json @@ -356,13 +356,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/sylph/nextflow_schema.json b/workflows/bactopia-tools/sylph/nextflow_schema.json index 738dcdbee..fde10b7a8 100644 --- a/workflows/bactopia-tools/sylph/nextflow_schema.json +++ b/workflows/bactopia-tools/sylph/nextflow_schema.json @@ -425,13 +425,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/tblastn/nextflow_schema.json b/workflows/bactopia-tools/tblastn/nextflow_schema.json index fe8a66e26..8553e48dd 100644 --- a/workflows/bactopia-tools/tblastn/nextflow_schema.json +++ b/workflows/bactopia-tools/tblastn/nextflow_schema.json @@ -401,13 +401,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/tblastx/nextflow_schema.json b/workflows/bactopia-tools/tblastx/nextflow_schema.json index 6b7e20c7c..3c98ac92e 100644 --- a/workflows/bactopia-tools/tblastx/nextflow_schema.json +++ b/workflows/bactopia-tools/tblastx/nextflow_schema.json @@ -401,13 +401,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/tbprofiler/nextflow_schema.json b/workflows/bactopia-tools/tbprofiler/nextflow_schema.json index f4f2c2d5c..625c98958 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow_schema.json +++ b/workflows/bactopia-tools/tbprofiler/nextflow_schema.json @@ -445,13 +445,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/bactopia-tools/traitar/nextflow_schema.json b/workflows/bactopia-tools/traitar/nextflow_schema.json index 623157972..ee43d606f 100644 --- a/workflows/bactopia-tools/traitar/nextflow_schema.json +++ b/workflows/bactopia-tools/traitar/nextflow_schema.json @@ -377,13 +377,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/cleanyerreads/nextflow_schema.json b/workflows/cleanyerreads/nextflow_schema.json index 374919178..ca3ffffc8 100644 --- a/workflows/cleanyerreads/nextflow_schema.json +++ b/workflows/cleanyerreads/nextflow_schema.json @@ -893,13 +893,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index 9bf28d0bd..46d3e6623 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -1457,13 +1457,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/workflows/teton/nextflow_schema.json b/workflows/teton/nextflow_schema.json index d453f7fa2..3cd95e952 100644 --- a/workflows/teton/nextflow_schema.json +++ b/workflows/teton/nextflow_schema.json @@ -776,13 +776,6 @@ "fa_icon": "far fa-clock", "hidden": true }, - "validate_params": { - "type": "boolean", - "default": true, - "fa_icon": "fas fa-tasks", - "description": "Boolean whether to validate parameters against the schema at runtime", - "hidden": true - }, "help": { "type": "boolean", "description": "Display help text.", From d2c948d2bacfa01e1e6c8380f908f02d93902166 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 28 Jul 2026 20:22:49 -0600 Subject: [PATCH 26/43] add new skills, start testing --- .../docs/project/01-repository-structure.md | 6 +- .claude/docs/project/04-testing-framework.md | 21 +- .claude/docs/reference/06-skills.md | 3 + .claude/docs/standards/02-logic-rules.md | 4 +- .../docs/standards/05-module-documentation.md | 25 +- .claude/skills/bump-versions/SKILL.md | 85 ++ .claude/skills/bump-versions/evals/evals.json | 23 + .../bump-versions/scripts/bump_versions.py | 158 +++ .claude/skills/release-checklist/SKILL.md | 247 ++++ .../skills/release-checklist/evals/evals.json | 44 + .../scripts/release_audit.py | 284 +++++ .claude/skills/review-tests/SKILL.md | 8 +- .claude/skills/run-tests/SKILL.md | 12 +- .claude/skills/update-datasets/SKILL.md | 95 ++ .../scripts/build-amrfinderplus-db.sh | 129 +++ .claude/skills/update-module/SKILL.md | 9 +- .gitignore | 2 + .vscode/settings.json | 6 + CHANGELOG.md | 55 +- CITATION.cff | 2 +- CLAUDE.md | 1 + bin/bactopia | 2 +- catalog.json | 63 +- conf/test_base.config | 26 + data/conda/meta.yaml | 2 +- llms.txt | 2 +- modules/abricate/run/tests/main.nf.test.snap | 2 +- modules/abricate/run/tests/nextflow.config | 19 +- .../abricate/summary/tests/main.nf.test.snap | 2 +- .../abricate/summary/tests/nextflow.config | 19 +- modules/abritamr/run/module.config | 6 +- modules/abritamr/run/tests/main.nf.test.snap | 8 +- modules/abritamr/run/tests/nextflow.config | 19 +- modules/agrvate/tests/main.nf.test.snap | 4 +- modules/agrvate/tests/nextflow.config | 19 +- .../amrfinderplus/run/tests/main.nf.test.snap | 4 +- .../amrfinderplus/run/tests/nextflow.config | 19 +- modules/amrfinderplus/update/main.nf | 59 - modules/amrfinderplus/update/module.config | 23 - modules/amrfinderplus/update/schema.json | 22 - modules/ariba/run/tests/main.nf.test.snap | 2 +- modules/ariba/run/tests/nextflow.config | 19 +- .../assembler/tests/main.nf.test.snap | 16 +- .../bactopia/assembler/tests/nextflow.config | 16 +- 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+- modules/hpsuissero/tests/nextflow.config | 19 +- modules/iqtree/module.config | 6 +- modules/iqtree/tests/main.nf.test.snap | 8 +- modules/iqtree/tests/nextflow.config | 19 +- modules/ismapper/tests/main.nf.test.snap | 2 +- modules/ismapper/tests/nextflow.config | 19 +- modules/kleborate/tests/main.nf.test.snap | 2 +- modules/kleborate/tests/nextflow.config | 19 +- modules/kraken2/tests/main.nf.test.snap | 8 +- modules/kraken2/tests/nextflow.config | 19 +- modules/legsta/tests/main.nf.test.snap | 2 +- modules/legsta/tests/nextflow.config | 19 +- modules/lissero/tests/main.nf.test.snap | 4 +- modules/lissero/tests/nextflow.config | 19 +- modules/mash/dist/module.config | 4 +- modules/mash/dist/tests/main.nf.test.snap | 4 +- modules/mash/dist/tests/nextflow.config | 19 +- modules/mashtree/tests/main.nf.test.snap | 2 +- modules/mashtree/tests/nextflow.config | 19 +- modules/mcroni/tests/main.nf.test.snap | 4 +- modules/mcroni/tests/nextflow.config | 19 +- modules/meningotype/tests/main.nf.test.snap | 4 +- modules/meningotype/tests/nextflow.config | 19 +- modules/merlin/dist/module.config | 4 +- modules/merlin/dist/tests/main.nf.test.snap | 4 +- modules/merlin/dist/tests/nextflow.config | 19 +- modules/midas/species/tests/main.nf.test.snap | 4 +- modules/midas/species/tests/nextflow.config | 19 +- modules/mlst/module.config | 6 +- modules/mlst/tests/main.nf.test.snap | 4 +- modules/mlst/tests/nextflow.config | 19 +- .../mobsuite/recon/tests/main.nf.test.snap | 8 +- modules/mobsuite/recon/tests/nextflow.config | 19 +- .../mykrobe/predict/tests/main.nf.test.snap | 2 +- modules/mykrobe/predict/tests/nextflow.config | 19 +- modules/ngmaster/module.config | 6 +- modules/ngmaster/tests/main.nf.test.snap | 8 +- modules/ngmaster/tests/nextflow.config | 19 +- modules/nohuman/download/module.config | 2 +- modules/nohuman/run/tests/main.nf.test.snap | 12 +- modules/nohuman/run/tests/nextflow.config | 19 +- modules/panaroo/run/module.config | 6 +- modules/panaroo/run/tests/main.nf.test.snap | 4 +- modules/panaroo/run/tests/nextflow.config | 19 +- modules/pasty/tests/main.nf.test.snap | 2 +- modules/pasty/tests/nextflow.config | 19 +- modules/pbptyper/tests/main.nf.test.snap | 2 +- modules/pbptyper/tests/nextflow.config | 19 +- modules/phispy/module.config | 6 +- modules/phispy/tests/main.nf.test.snap | 4 +- modules/phispy/tests/nextflow.config | 19 +- modules/pirate/tests/main.nf.test.snap | 2 +- modules/pirate/tests/nextflow.config | 19 +- modules/plasmidfinder/tests/main.nf.test.snap | 4 +- modules/plasmidfinder/tests/nextflow.config | 19 +- modules/pneumocat/tests/main.nf.test.snap | 2 +- modules/pneumocat/tests/nextflow.config | 19 +- modules/prokka/tests/main.nf.test.snap | 6 +- modules/prokka/tests/nextflow.config | 19 +- modules/quast/tests/main.nf.test.snap | 6 +- modules/quast/tests/nextflow.config | 19 +- modules/rgi/heatmap/module.config | 6 +- modules/rgi/heatmap/tests/main.nf.test.snap | 4 +- modules/rgi/heatmap/tests/nextflow.config | 19 +- modules/rgi/main/main.nf | 2 +- modules/rgi/main/module.config | 10 +- modules/rgi/main/schema.json | 4 +- modules/rgi/main/tests/main.nf.test | 31 + modules/rgi/main/tests/main.nf.test.snap | 33 +- modules/rgi/main/tests/nextflow.config | 19 +- modules/roary/tests/main.nf.test.snap | 2 +- modules/roary/tests/nextflow.config | 19 +- modules/sccmec/tests/main.nf.test.snap | 4 +- modules/sccmec/tests/nextflow.config | 19 +- modules/scoary/tests/main.nf.test.snap | 2 +- modules/scoary/tests/nextflow.config | 19 +- modules/seqsero2/tests/main.nf.test.snap | 4 +- modules/seqsero2/tests/nextflow.config | 19 +- modules/seroba/run/tests/main.nf.test.snap | 2 +- modules/seroba/run/tests/nextflow.config | 19 +- modules/shigapass/tests/main.nf.test.snap | 4 +- modules/shigapass/tests/nextflow.config | 19 +- modules/shigatyper/tests/main.nf.test.snap | 2 +- modules/shigatyper/tests/nextflow.config | 19 +- modules/shigeifinder/tests/main.nf.test.snap | 4 +- modules/shigeifinder/tests/nextflow.config | 19 +- modules/sistr/tests/main.nf.test.snap | 4 +- modules/sistr/tests/nextflow.config | 19 +- modules/snippy/core/tests/main.nf.test.snap | 2 +- modules/snippy/core/tests/nextflow.config | 19 +- modules/snippy/run/tests/main.nf.test.snap | 4 +- modules/snippy/run/tests/nextflow.config | 19 +- modules/snpdists/tests/main.nf.test.snap | 2 +- modules/snpdists/tests/nextflow.config | 19 +- modules/spatyper/tests/main.nf.test.snap | 4 +- modules/spatyper/tests/nextflow.config | 19 +- .../scrub/tests/main.nf.test.snap | 4 +- .../scrub/tests/nextflow.config | 19 +- modules/ssuissero/tests/main.nf.test.snap | 4 +- modules/ssuissero/tests/nextflow.config | 19 +- .../staphopiasccmec/tests/main.nf.test.snap | 4 +- modules/staphopiasccmec/tests/nextflow.config | 19 +- modules/staphscan/module.config | 6 +- modules/staphscan/tests/main.nf.test.snap | 6 +- modules/staphscan/tests/nextflow.config | 19 +- modules/stecfinder/tests/main.nf.test.snap | 6 +- modules/stecfinder/tests/nextflow.config | 19 +- modules/stxtyper/tests/main.nf.test.snap | 2 +- modules/stxtyper/tests/nextflow.config | 19 +- modules/sylph/profile/tests/main.nf.test.snap | 4 +- modules/sylph/profile/tests/nextflow.config | 16 +- .../collate/tests/main.nf.test.snap | 2 +- .../tbprofiler/collate/tests/nextflow.config | 19 +- .../profile/tests/main.nf.test.snap | 6 +- .../tbprofiler/profile/tests/nextflow.config | 19 +- modules/traitar/run/tests/main.nf.test.snap | 4 +- modules/traitar/run/tests/nextflow.config | 19 +- nextflow.config | 4 +- nextflow_schema.json | 6 - subworkflows/abricate/tests/main.nf.test.snap | 2 +- subworkflows/abricate/tests/nextflow.config | 20 +- subworkflows/abritamr/tests/main.nf.test.snap | 4 +- subworkflows/abritamr/tests/nextflow.config | 20 +- subworkflows/agrvate/tests/main.nf.test.snap | 2 +- subworkflows/agrvate/tests/nextflow.config | 20 +- .../amrfinderplus/tests/main.nf.test.snap | 2 +- .../amrfinderplus/tests/nextflow.config | 20 +- subworkflows/ariba/tests/main.nf.test.snap | 2 +- subworkflows/ariba/tests/nextflow.config | 20 +- .../bactopia/assembler/tests/nextflow.config | 20 +- .../bactopia/datasets/tests/nextflow.config | 21 +- .../bactopia/qc/tests/nextflow.config | 23 +- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- .../bactopia/sketcher/tests/nextflow.config | 20 +- subworkflows/bakta/tests/main.nf.test.snap | 2 +- subworkflows/bakta/tests/nextflow.config | 20 +- subworkflows/blastn/tests/main.nf.test.snap | 2 +- subworkflows/blastn/tests/nextflow.config | 20 +- subworkflows/blastp/tests/main.nf.test.snap | 2 +- subworkflows/blastp/tests/nextflow.config | 20 +- subworkflows/blastx/tests/main.nf.test.snap | 2 +- subworkflows/blastx/tests/nextflow.config | 20 +- subworkflows/bracken/tests/nextflow.config | 20 +- subworkflows/btyper3/tests/main.nf.test.snap | 2 +- subworkflows/btyper3/tests/nextflow.config | 20 +- subworkflows/busco/tests/main.nf.test.snap | 4 +- subworkflows/busco/tests/nextflow.config | 20 +- subworkflows/checkm/tests/main.nf.test.snap | 2 +- subworkflows/checkm/tests/nextflow.config | 20 +- subworkflows/checkm2/tests/main.nf.test.snap | 2 +- subworkflows/checkm2/tests/nextflow.config | 20 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/nextflow.config | 20 +- .../clonalframeml/tests/main.nf.test.snap | 4 +- .../clonalframeml/tests/nextflow.config | 20 +- subworkflows/deacon/tests/main.nf.test.snap | 2 +- subworkflows/deacon/tests/nextflow.config | 20 +- .../defensefinder/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/nextflow.config | 20 +- subworkflows/ectyper/tests/main.nf.test.snap | 2 +- subworkflows/ectyper/tests/nextflow.config | 20 +- subworkflows/eggnog/tests/main.nf.test.snap | 4 +- subworkflows/eggnog/tests/nextflow.config | 20 +- subworkflows/emmtyper/tests/main.nf.test.snap | 2 +- subworkflows/emmtyper/tests/nextflow.config | 20 +- subworkflows/fastani/tests/main.nf.test.snap | 2 +- subworkflows/fastani/tests/nextflow.config | 20 +- subworkflows/gamma/tests/main.nf.test.snap | 2 +- subworkflows/gamma/tests/nextflow.config | 20 +- subworkflows/genomedl/tests/main.nf.test.snap | 6 +- subworkflows/genomedl/tests/nextflow.config | 20 +- .../genotyphi/tests/main.nf.test.snap | 2 +- subworkflows/genotyphi/tests/nextflow.config | 20 +- .../gigatyper/tests/main.nf.test.snap | 2 +- subworkflows/gigatyper/tests/nextflow.config | 20 +- subworkflows/gtdb/tests/main.nf.test.snap | 4 +- subworkflows/gtdb/tests/nextflow.config | 20 +- subworkflows/gubbins/tests/main.nf.test.snap | 2 +- subworkflows/gubbins/tests/nextflow.config | 20 +- subworkflows/hicap/tests/main.nf.test.snap | 2 +- subworkflows/hicap/tests/nextflow.config | 20 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- subworkflows/hpsuissero/tests/nextflow.config | 20 +- subworkflows/iqtree/tests/main.nf.test.snap | 4 +- subworkflows/iqtree/tests/nextflow.config | 20 +- subworkflows/ismapper/tests/main.nf.test.snap | 2 +- subworkflows/ismapper/tests/nextflow.config | 20 +- .../kleborate/tests/main.nf.test.snap | 2 +- subworkflows/kleborate/tests/nextflow.config | 20 +- subworkflows/kraken2/tests/main.nf.test.snap | 4 +- subworkflows/kraken2/tests/nextflow.config | 20 +- subworkflows/legsta/tests/main.nf.test.snap | 2 +- subworkflows/legsta/tests/nextflow.config | 20 +- subworkflows/lissero/tests/main.nf.test.snap | 2 +- subworkflows/lissero/tests/nextflow.config | 20 +- subworkflows/mashdist/tests/main.nf.test.snap | 2 +- subworkflows/mashdist/tests/nextflow.config | 20 +- subworkflows/mashtree/tests/main.nf.test.snap | 2 +- subworkflows/mashtree/tests/nextflow.config | 20 +- subworkflows/mcroni/tests/main.nf.test.snap | 2 +- subworkflows/mcroni/tests/nextflow.config | 20 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../meningotype/tests/nextflow.config | 20 +- subworkflows/merlin/tests/main.nf.test | 1 + subworkflows/merlin/tests/nextflow.config | 21 +- .../merlindist/tests/main.nf.test.snap | 2 +- subworkflows/merlindist/tests/nextflow.config | 20 +- subworkflows/midas/tests/main.nf.test.snap | 2 +- subworkflows/midas/tests/nextflow.config | 20 +- subworkflows/mlst/tests/main.nf.test.snap | 4 +- subworkflows/mlst/tests/nextflow.config | 20 +- subworkflows/mobsuite/tests/main.nf.test.snap | 2 +- subworkflows/mobsuite/tests/nextflow.config | 20 +- subworkflows/mykrobe/tests/main.nf.test.snap | 2 +- subworkflows/mykrobe/tests/nextflow.config | 20 +- subworkflows/ngmaster/tests/main.nf.test.snap | 4 +- subworkflows/ngmaster/tests/nextflow.config | 20 +- subworkflows/nohuman/tests/main.nf.test.snap | 4 +- subworkflows/nohuman/tests/nextflow.config | 20 +- subworkflows/panaroo/tests/main.nf.test.snap | 4 +- subworkflows/panaroo/tests/nextflow.config | 20 +- .../pangenome/tests/main.nf.test.snap | 4 +- subworkflows/pangenome/tests/nextflow.config | 20 +- subworkflows/pasty/tests/main.nf.test.snap | 2 +- subworkflows/pasty/tests/nextflow.config | 20 +- subworkflows/pbptyper/tests/main.nf.test.snap | 2 +- subworkflows/pbptyper/tests/nextflow.config | 20 +- subworkflows/phispy/tests/main.nf.test.snap | 4 +- subworkflows/phispy/tests/nextflow.config | 20 +- subworkflows/pirate/tests/main.nf.test.snap | 2 +- subworkflows/pirate/tests/nextflow.config | 20 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/nextflow.config | 20 +- .../pneumocat/tests/main.nf.test.snap | 2 +- subworkflows/pneumocat/tests/nextflow.config | 20 +- subworkflows/prokka/tests/main.nf.test.snap | 2 +- subworkflows/prokka/tests/nextflow.config | 20 +- subworkflows/quast/tests/main.nf.test.snap | 2 +- subworkflows/quast/tests/nextflow.config | 20 +- subworkflows/rgi/tests/main.nf.test.snap | 6 +- subworkflows/rgi/tests/nextflow.config | 20 +- subworkflows/roary/tests/main.nf.test.snap | 2 +- subworkflows/roary/tests/nextflow.config | 20 +- subworkflows/sccmec/tests/main.nf.test.snap | 2 +- subworkflows/sccmec/tests/nextflow.config | 20 +- subworkflows/scoary/tests/main.nf.test.snap | 2 +- subworkflows/scoary/tests/nextflow.config | 20 +- subworkflows/scrubber/tests/main.nf.test.snap | 39 +- subworkflows/scrubber/tests/nextflow.config | 20 +- subworkflows/seqsero2/tests/main.nf.test.snap | 2 +- subworkflows/seqsero2/tests/nextflow.config | 20 +- subworkflows/seroba/tests/main.nf.test.snap | 2 +- subworkflows/seroba/tests/nextflow.config | 20 +- .../shigapass/tests/main.nf.test.snap | 2 +- subworkflows/shigapass/tests/nextflow.config | 20 +- .../shigatyper/tests/main.nf.test.snap | 2 +- subworkflows/shigatyper/tests/nextflow.config | 20 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- .../shigeifinder/tests/nextflow.config | 20 +- subworkflows/sistr/tests/main.nf.test.snap | 2 +- subworkflows/sistr/tests/nextflow.config | 20 +- .../snippy/core/tests/main.nf.test.snap | 2 +- .../snippy/core/tests/nextflow.config | 20 +- .../snippy/run/tests/main.nf.test.snap | 2 +- subworkflows/snippy/run/tests/nextflow.config | 20 +- subworkflows/snpdists/tests/main.nf.test.snap | 2 +- subworkflows/snpdists/tests/nextflow.config | 20 +- subworkflows/spatyper/tests/main.nf.test.snap | 2 +- subworkflows/spatyper/tests/nextflow.config | 20 +- .../srahumanscrubber/tests/main.nf.test.snap | 2 +- .../srahumanscrubber/tests/nextflow.config | 20 +- .../ssuissero/tests/main.nf.test.snap | 2 +- subworkflows/ssuissero/tests/nextflow.config | 20 +- .../staphopiasccmec/tests/main.nf.test.snap | 2 +- .../staphopiasccmec/tests/nextflow.config | 20 +- .../staphscan/tests/main.nf.test.snap | 6 +- subworkflows/staphscan/tests/nextflow.config | 20 +- subworkflows/staphtyper/tests/main.nf.test | 1 + subworkflows/staphtyper/tests/nextflow.config | 21 +- subworkflows/stecfinder/main.nf | 3 +- .../stecfinder/tests/main.nf.test.snap | 2 +- subworkflows/stecfinder/tests/nextflow.config | 20 +- subworkflows/stxtyper/tests/main.nf.test.snap | 2 +- subworkflows/stxtyper/tests/nextflow.config | 20 +- subworkflows/sylph/tests/main.nf.test.snap | 2 +- subworkflows/sylph/tests/nextflow.config | 20 +- subworkflows/tblastn/tests/main.nf.test.snap | 2 +- subworkflows/tblastn/tests/nextflow.config | 20 +- subworkflows/tblastx/tests/main.nf.test.snap | 2 +- subworkflows/tblastx/tests/nextflow.config | 20 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- subworkflows/tbprofiler/tests/nextflow.config | 20 +- subworkflows/teton/tests/main.nf.test | 7 +- subworkflows/teton/tests/main.nf.test.snap | 6 +- subworkflows/teton/tests/nextflow.config | 20 +- subworkflows/traitar/tests/main.nf.test.snap | 2 +- subworkflows/traitar/tests/nextflow.config | 20 +- tests/main.nf.test.snap | 1027 +---------------- versions.yml | 2 + .../bactopia-tools/abricate/nextflow.config | 4 +- .../abricate/tests/main.nf.test.snap | 2 +- .../bactopia-tools/abritamr/nextflow.config | 4 +- .../abritamr/tests/main.nf.test.snap | 4 +- .../bactopia-tools/agrvate/nextflow.config | 4 +- .../agrvate/tests/main.nf.test.snap | 4 +- .../amrfinderplus/nextflow.config | 4 +- .../amrfinderplus/tests/main.nf.test.snap | 6 +- .../bactopia-tools/ariba/nextflow.config | 4 +- .../ariba/tests/main.nf.test.snap | 2 +- .../bactopia-tools/bakta/nextflow.config | 4 +- .../bakta/tests/main.nf.test.snap | 4 +- .../bactopia-tools/blastn/nextflow.config | 4 +- .../blastn/tests/main.nf.test.snap | 6 +- .../bactopia-tools/blastp/nextflow.config | 4 +- .../blastp/tests/main.nf.test.snap | 6 +- .../bactopia-tools/blastx/nextflow.config | 4 +- .../blastx/tests/main.nf.test.snap | 6 +- .../bactopia-tools/bracken/nextflow.config | 4 +- .../bracken/tests/main.nf.test.snap | 16 +- .../bactopia-tools/btyper3/nextflow.config | 4 +- .../btyper3/tests/main.nf.test.snap | 2 +- .../bactopia-tools/busco/nextflow.config | 4 +- .../busco/tests/main.nf.test.snap | 8 +- .../bactopia-tools/checkm/nextflow.config | 4 +- .../checkm/tests/main.nf.test.snap | 2 +- .../bactopia-tools/checkm2/nextflow.config | 4 +- .../checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/nextflow.config | 4 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../defensefinder/nextflow.config | 4 +- .../defensefinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ectyper/nextflow.config | 4 +- .../ectyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/eggnog/nextflow.config | 4 +- .../eggnog/tests/main.nf.test.snap | 4 +- .../bactopia-tools/emmtyper/nextflow.config | 4 +- .../emmtyper/tests/main.nf.test.snap | 4 +- .../bactopia-tools/fastani/nextflow.config | 4 +- .../fastani/tests/main.nf.test.snap | 6 +- .../bactopia-tools/gamma/nextflow.config | 4 +- .../gamma/tests/main.nf.test.snap | 2 +- .../bactopia-tools/genotyphi/nextflow.config | 4 +- .../genotyphi/tests/main.nf.test.snap | 2 +- .../bactopia-tools/gigatyper/nextflow.config | 4 +- .../gigatyper/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 4 +- .../gtdb/tests/main.nf.test.snap | 4 +- .../bactopia-tools/hicap/nextflow.config | 4 +- .../hicap/tests/main.nf.test.snap | 2 +- .../bactopia-tools/hpsuissero/nextflow.config | 4 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ismapper/nextflow.config | 4 +- .../ismapper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/kleborate/nextflow.config | 4 +- .../kleborate/tests/main.nf.test.snap | 2 +- .../bactopia-tools/kraken2/nextflow.config | 4 +- .../kraken2/tests/main.nf.test.snap | 10 +- .../bactopia-tools/legsta/nextflow.config | 4 +- .../legsta/tests/main.nf.test.snap | 2 +- .../bactopia-tools/lissero/nextflow.config | 4 +- .../lissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mashdist/nextflow.config | 4 +- .../mashdist/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mashtree/nextflow.config | 4 +- .../mashtree/tests/main.nf.test.snap | 4 +- .../bactopia-tools/mcroni/nextflow.config | 4 +- .../mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/nextflow.config | 4 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../bactopia-tools/merlin/nextflow.config | 4 +- .../merlin/tests/main.nf.test.snap | 4 +- .../bactopia-tools/midas/nextflow.config | 4 +- .../midas/tests/main.nf.test.snap | 4 +- workflows/bactopia-tools/mlst/nextflow.config | 4 +- .../mlst/tests/main.nf.test.snap | 4 +- .../bactopia-tools/mobsuite/nextflow.config | 4 +- .../mobsuite/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mykrobe/nextflow.config | 4 +- .../mykrobe/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ngmaster/nextflow.config | 4 +- .../ngmaster/tests/main.nf.test.snap | 4 +- .../bactopia-tools/pangenome/nextflow.config | 4 +- .../bactopia-tools/pangenome/tests/.nftignore | 1 + .../pangenome/tests/main.nf.test.snap | 41 +- .../bactopia-tools/pasty/nextflow.config | 4 +- .../pasty/tests/main.nf.test.snap | 2 +- .../bactopia-tools/pbptyper/nextflow.config | 4 +- .../pbptyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/phispy/nextflow.config | 4 +- .../phispy/tests/main.nf.test.snap | 6 +- .../plasmidfinder/nextflow.config | 4 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/pneumocat/nextflow.config | 4 +- .../pneumocat/tests/main.nf.test.snap | 2 +- .../bactopia-tools/prokka/nextflow.config | 4 +- .../prokka/tests/main.nf.test.snap | 2 +- .../bactopia-tools/quast/nextflow.config | 4 +- .../quast/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 4 +- .../bactopia-tools/rgi/nextflow_schema.json | 4 +- .../rgi/tests/main.nf.test.snap | 18 +- .../bactopia-tools/sccmec/nextflow.config | 4 +- .../sccmec/tests/main.nf.test.snap | 4 +- .../bactopia-tools/scrubber/nextflow.config | 4 +- .../scrubber/tests/main.nf.test.snap | 6 +- .../bactopia-tools/seqsero2/nextflow.config | 4 +- .../seqsero2/tests/main.nf.test.snap | 2 +- .../bactopia-tools/seroba/nextflow.config | 4 +- .../seroba/tests/main.nf.test.snap | 2 +- .../bactopia-tools/shigapass/nextflow.config | 4 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../bactopia-tools/shigatyper/nextflow.config | 4 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/nextflow.config | 4 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/sistr/nextflow.config | 4 +- .../sistr/tests/main.nf.test.snap | 2 +- .../bactopia-tools/snippy/nextflow.config | 4 +- .../snippy/tests/main.nf.test.snap | 14 +- .../bactopia-tools/spatyper/nextflow.config | 4 +- .../spatyper/tests/main.nf.test.snap | 4 +- .../bactopia-tools/ssuissero/nextflow.config | 4 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/staphscan/nextflow.config | 4 +- .../staphscan/tests/main.nf.test.snap | 8 +- .../bactopia-tools/staphtyper/nextflow.config | 4 +- .../staphtyper/tests/main.nf.test.snap | 8 +- .../bactopia-tools/stecfinder/nextflow.config | 4 +- .../stecfinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/stxtyper/nextflow.config | 4 +- .../stxtyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/sylph/nextflow.config | 4 +- .../sylph/tests/main.nf.test.snap | 2 +- .../bactopia-tools/tblastn/nextflow.config | 4 +- .../tblastn/tests/main.nf.test.snap | 4 +- .../bactopia-tools/tblastx/nextflow.config | 4 +- .../tblastx/tests/main.nf.test.snap | 6 +- .../bactopia-tools/tbprofiler/nextflow.config | 4 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- .../bactopia-tools/traitar/nextflow.config | 4 +- .../traitar/tests/main.nf.test.snap | 2 +- workflows/cleanyerreads/nextflow.config | 4 +- workflows/cleanyerreads/nextflow_schema.json | 6 - .../cleanyerreads/tests/main.nf.test.snap | 8 +- workflows/staphopia/nextflow.config | 4 +- workflows/staphopia/nextflow_schema.json | 6 - workflows/staphopia/tests/main.nf.test.snap | 10 +- workflows/teton/nextflow.config | 4 +- workflows/teton/nextflow_schema.json | 6 - workflows/teton/tests/main.nf.test.snap | 12 +- 575 files changed, 2185 insertions(+), 5380 deletions(-) create mode 100644 .claude/skills/bump-versions/SKILL.md create mode 100644 .claude/skills/bump-versions/evals/evals.json create mode 100755 .claude/skills/bump-versions/scripts/bump_versions.py create mode 100644 .claude/skills/release-checklist/SKILL.md create mode 100644 .claude/skills/release-checklist/evals/evals.json create mode 100755 .claude/skills/release-checklist/scripts/release_audit.py create mode 100644 .claude/skills/update-datasets/SKILL.md create mode 100755 .claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh create mode 100644 conf/test_base.config delete mode 100644 modules/amrfinderplus/update/main.nf delete mode 100644 modules/amrfinderplus/update/module.config delete mode 100644 modules/amrfinderplus/update/schema.json create mode 100644 versions.yml diff --git a/.claude/docs/project/01-repository-structure.md b/.claude/docs/project/01-repository-structure.md index b1bb8fd96..81b0eaacf 100644 --- a/.claude/docs/project/01-repository-structure.md +++ b/.claude/docs/project/01-repository-structure.md @@ -39,7 +39,7 @@ bactopia/ - `main.nf` - Process definition with GroovyDoc documentation - `module.config` - Module parameters and process configuration - `schema.json` - Parameter schema for validation -- **Count**: 98 modules +- **Count**: 104 modules - **Examples**: `abricate/`, `prokka/`, `kraken2/` ### `/subworkflows/` (Tier 2) @@ -50,7 +50,7 @@ bactopia/ - `{tool}/` - Tool-specific processing logic - **Contents**: - `main.nf` - Subworkflow definition with GroovyDoc documentation -- **Count**: 89 subworkflows +- **Count**: 93 subworkflows - **Key Requirement**: Emit two record channels — `sample_outputs` (module record passthrough) and `run_outputs` (aggregated results) ### `/workflows/` (Tier 1) @@ -152,7 +152,7 @@ Results (record channels: sample_outputs + run_outputs) ### Workflow Organization - Entry points in root directory -- Bactopia Tools in `workflows/bactopia-tools/` (67 tools; 71 workflows total across all tiers) +- Bactopia Tools in `workflows/bactopia-tools/` (70 tools; 74 workflows total across all tiers) - Named workflows as separate directories under `workflows/`: - `workflows/cleanyerreads/` - Read cleaning workflow - `workflows/staphopia/` - Staphylococcus-focused analysis diff --git a/.claude/docs/project/04-testing-framework.md b/.claude/docs/project/04-testing-framework.md index 2ca889ed0..6a43d99c8 100644 --- a/.claude/docs/project/04-testing-framework.md +++ b/.claude/docs/project/04-testing-framework.md @@ -69,6 +69,7 @@ config { // Minimal config for module-level testing nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -78,25 +79,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" @@ -105,7 +88,7 @@ includeConfig "../../../conf/profiles.config" ``` > `params.workflow.ext` is a **string** at module-test scope (a single extension for the module's primary output). Workflow-level configs (`workflows/{name}/nextflow.config`) use the **list** form — e.g. `ext = ['fna']` — because workflows aggregate publishing across multiple module outputs. Match the surrounding layer when editing. -> `bactopia_version` is a placeholder — keep it in sync with the repo's `manifest.version` in [nextflow.config](../../../nextflow.config) when it drifts. +> The pipeline version and the `nf-bactopia@` plugin pin are **not** repeated per test config — they live in [conf/test_base.config](../../../conf/test_base.config), included at the top of every test config, and are propagated from `versions.yml` by `/bump-versions`. Only per-component params (`workflow{}`, `wf`, and any resource or tool-specific overrides) stay local. ## Writing Tests diff --git a/.claude/docs/reference/06-skills.md b/.claude/docs/reference/06-skills.md index 24ce980c3..702faee96 100644 --- a/.claude/docs/reference/06-skills.md +++ b/.claude/docs/reference/06-skills.md @@ -13,14 +13,17 @@ Skills are AI tooling — short instruction files that Claude invokes via the `S | [add-bactopia-tool](../../skills/add-bactopia-tool/) | `bactopia-scaffold` | Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. | | [add-module](../../skills/add-module/) | `bactopia-scaffold` | Scaffold a new Bactopia module from a bioconda/conda-forge package. | | [add-subworkflow](../../skills/add-subworkflow/) | `bactopia-scaffold` | Scaffold a new Bactopia subworkflow that orchestrates existing modules. | +| [bump-versions](../../skills/bump-versions/) | — | Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/test_base.config, CITATION.cff, bin/bactopia, data/conda/meta.yaml). | | [merge-schemas](../../skills/merge-schemas/) | `bactopia-merge-schemas` | Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows by running bactopia-merge-schemas. | | [project-status](../../skills/project-status/) | `bactopia-status` | Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues. | +| [release-checklist](../../skills/release-checklist/) | — | Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report. | | [review-citations](../../skills/review-citations/) | `bactopia-citations` | Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate. | | [review-docs](../../skills/review-docs/) | `bactopia-docs` | Review staleness of reference docs under .claude/docs/ using bactopia-docs --validate. | | [review-groovydoc](../../skills/review-groovydoc/) | `bactopia-lint` | Review GroovyDoc accuracy across modules and subworkflows using bactopia-lint. | | [review-tests](../../skills/review-tests/) | — | Review nf-test run results and present a diagnostic summary with grouped error analysis. | | [run-tests](../../skills/run-tests/) | `bactopia-test` | Run Bactopia nf-tests via bactopia-test and produce a timestamped logs/ directory that /review-tests can interpret. | | [update-catalog](../../skills/update-catalog/) | `bactopia-catalog` | Regenerate catalog.json and llms.txt by running bactopia-catalog. | +| [update-datasets](../../skills/update-datasets/) | — | Build and publish Bactopia's version-pinned datasets to Cloudflare R2. | | [update-module](../../skills/update-module/) | `bactopia-update` | Check for newer versions of tools used in Bactopia modules and apply updates to module.config files and CHANGELOG.md. | The `Purpose` column is the first sentence of each skill's `description:` frontmatter. Drift between the table and the source file is caught by **D107** in `/review-docs`. Full trigger-phrase lists live in each `SKILL.md` — read it directly when you need the exact phrasing. diff --git a/.claude/docs/standards/02-logic-rules.md b/.claude/docs/standards/02-logic-rules.md index 039aa7657..61389d342 100644 --- a/.claude/docs/standards/02-logic-rules.md +++ b/.claude/docs/standards/02-logic-rules.md @@ -40,7 +40,7 @@ This guide defines the decision-making logic and taxonomy used to classify Bacto - **Definition**: No sample/data channels in the `take` block - **Use case**: Utility modules that download resources or perform setup tasks - **Note**: May have `Path`, `Value`, or other non-channel parameters but no `Channel` inputs -- **Examples**: wget, ariba/getref, bactopia/datasets, amrfinderplus/update +- **Examples**: wget, ariba/getref, bactopia/datasets ### Single Input - **Definition**: The `take` block defines exactly **1 Channel** @@ -119,7 +119,7 @@ This guide defines the decision-making logic and taxonomy used to classify Bacto #### internet-access - Requires active internet connection during execution - **Key indicators**: External URLs, download commands (wget, curl) -- Examples: gather (SRA download), amrfinderplus/update +- Examples: gather (SRA download), wget #### alternative-execution - Multiple tool options for the same task diff --git a/.claude/docs/standards/05-module-documentation.md b/.claude/docs/standards/05-module-documentation.md index d28aec436..ab4151b44 100644 --- a/.claude/docs/standards/05-module-documentation.md +++ b/.claude/docs/standards/05-module-documentation.md @@ -89,7 +89,7 @@ Bactopia modules are individual process definitions that execute specific bioinf - **Definition**: No sample/data channels; only parameters - **Pattern**: No record input block; may accept simple `Path` or `String` parameters - **Use Case**: Utility modules for downloads, database setup, or internal maintenance -- **Examples**: wget, ariba/getref, bactopia/datasets, amrfinderplus/update +- **Examples**: wget, ariba/getref, bactopia/datasets #### Single Input - **Definition**: One primary data channel (plus parameters) @@ -554,7 +554,7 @@ Some tools are split across multiple modules (e.g., bakta/download, bakta/run): ### 8.4 Utility/Setup Modules Some modules are used for setup, downloading, or internal maintenance tasks rather than sample processing. These modules may have non-standard output structures: -**Examples**: `wget`, `ariba/getref`, `amrfinderplus/update`, `bakta/download`, `bactopia/datasets` +**Examples**: `wget`, `ariba/getref`, `bakta/download`, `bactopia/datasets` **Characteristics**: - May not include `nf_logs` and `versions` as separate outputs (logs may be bundled in a subdirectory) @@ -926,6 +926,7 @@ nextflow_process { // Minimal config for module-level testing nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -935,25 +936,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" @@ -961,6 +944,8 @@ includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" ``` +`bactopia_version` and the `nf-bactopia@` plugin pin are inherited from [conf/test_base.config](../../../conf/test_base.config) (included at the top) — do not repeat them per file. `/bump-versions` propagates `versions.yml` into that single file. + **Path depth for multi-process modules:** Use `../../../../conf/` instead of `../../../conf/` since the module.config is one level deeper (e.g., `modules/bakta/run/tests/nextflow.config`). ### 11.4 nf-test.config Template diff --git a/.claude/skills/bump-versions/SKILL.md b/.claude/skills/bump-versions/SKILL.md new file mode 100644 index 000000000..174af69f3 --- /dev/null +++ b/.claude/skills/bump-versions/SKILL.md @@ -0,0 +1,85 @@ +--- +name: bump-versions +description: Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/test_base.config, CITATION.cff, bin/bactopia, data/conda/meta.yaml). Use this whenever the user has edited versions.yml and wants the rest of the repo brought in line, or asks to bump the version, set the release version, propagate versions.yml, sync version-bearing files, fix a V001 version-consistency failure, or prepare version files for a release. This never edits versions.yml itself and never regenerates the templated artifacts (nextflow.config, catalog.json) — it hands those off to /merge-schemas and /update-catalog. +--- + +# Bump Versions + +`versions.yml` at the repo root is the **single source of truth** for the pipeline +version (`bactopia`) and the plugin pin (`nf-bactopia`). It is edited **by hand** — +this skill never touches it. Its job is the mechanical, error-prone part: copying +those two values into every *hand-maintained* file that repeats them, so +bactopia-lint's **V001** (version-bearing files must equal `versions.yml`) goes green. + +Two classes of version-bearing files exist, and only one is this skill's concern: + +- **Hand-maintained (this skill fixes these):** `conf/test_base.config` + (`bactopia_version` + the `nf-bactopia@` plugin pin, inherited by all ~183 + module/subworkflow test configs), `CITATION.cff`, `bin/bactopia`, + `data/conda/meta.yaml`. +- **Generated (this skill does NOT touch these):** `nextflow.config`, every + `workflows/*/nextflow.config`, `catalog.json`, `llms.txt`. These are rendered + from `versions.yml` by `bactopia-merge-schemas` / `bactopia-catalog`, so the fix + is to *regenerate* them — a follow-up, not an edit. Slash commands cannot invoke + other slash commands, so you recommend those to the user rather than running them. + +## Steps + +1. **Dry-run first.** Show the user exactly what will change before writing anything: + ``` + python3 .claude/skills/bump-versions/scripts/bump_versions.py \ + --bactopia-path /home/rpetit3/repos/bactopia/bactopia --check + ``` + The script reads `versions.yml`, then reports each hand-maintained literal as + `would update -> `, `already `, or a `WARN` (file missing or + the literal moved). If everything is already `ok`, tell the user the + hand-maintained files are in sync and skip to step 4 (they may still need a + regen if a generated artifact lagged). + +2. **Confirm, then apply.** Once the user is happy with the dry-run, drop `--check` + to write the changes: + ``` + python3 .claude/skills/bump-versions/scripts/bump_versions.py \ + --bactopia-path /home/rpetit3/repos/bactopia/bactopia + ``` + Only the version token inside each match is rewritten; runs are idempotent. + +3. **Recommend the regeneration follow-ups.** If anything changed (or a generated + artifact is suspected stale), tell the user to run, in order: + - `/merge-schemas all` — re-renders `nextflow.config` + workflow configs + schemas from `versions.yml`. + - `/update-catalog` — rebuilds `catalog.json` + `llms.txt`. + Do not attempt to run these from here. + +4. **Verify V001–V003.** Confirm the version gate is actually green: + ``` + bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh \ + --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent + ``` + Read the `repo` component's results. A clean run lists **no** `V0xx` failures + (PASS results are suppressed). If **V001** still fails, report the offending + files verbatim — most often a generated artifact whose regen (step 3) hasn't run + yet, or a version-bearing file this skill doesn't own. + +5. **Flag downstream checks (report, don't fix):** + - **V002** compares `versions.yml` to the top `## vX.Y.Z` CHANGELOG heading. If + they disagree, the CHANGELOG needs a section for the new version — that's + human-authored content, so surface it, don't invent it. + - Bumping `bactopia_version` changes the test container tag + (`bactopia/bactopia:`) used by every module/subworkflow test. Recommend + a smoke test (`/run-tests` on a quick component) once the matching image exists, + since a nonexistent tag will fail tests even with a green lint. + +## Notes + +- The script needs only Python stdlib + read access to `versions.yml`; no conda env + or `bactopia-*` CLI. There is deliberately **no** `bactopia-versions` CLI — + `versions.yml` is hand-edited and this propagation is the whole story. +- The four hand-maintained targets and their literal formats are encoded in the + script's `TARGETS` map, matching V001's own regexes so the skill fixes exactly what + the linter checks. If V001 ever grows a new hand-maintained file, add it there. + +### Sibling skills + +- `/merge-schemas`, `/update-catalog` — the regeneration follow-ups (step 3). +- `/review-groovydoc` — backs the `bactopia-lint` verification run (step 4). +- `/release-checklist` — its check 1 delegates the version gate to these same V-rules. diff --git a/.claude/skills/bump-versions/evals/evals.json b/.claude/skills/bump-versions/evals/evals.json new file mode 100644 index 000000000..46d538b91 --- /dev/null +++ b/.claude/skills/bump-versions/evals/evals.json @@ -0,0 +1,23 @@ +{ + "skill_name": "bump-versions", + "evals": [ + { + "id": 1, + "prompt": "I just bumped versions.yml to bactopia 4.1.0. Can you get the rest of the repo's version files in sync?", + "expected_output": "Runs bump_versions.py --check, shows the dry-run (conf/test_base.config bactopia_version 4.0.0 -> 4.1.0, others already current), applies after confirmation, then recommends /merge-schemas + /update-catalog and verifying V001, without editing versions.yml.", + "files": [] + }, + { + "id": 2, + "prompt": "release-checklist says V001 is failing on conf/test_base.config, the version doesn't match versions.yml. Fix it.", + "expected_output": "Identifies this as a version-propagation task, dry-runs and applies bump_versions.py to bring conf/test_base.config in line with versions.yml, re-runs bactopia-lint to confirm V001 passes, and flags that generated artifacts may still need /merge-schemas + /update-catalog.", + "files": [] + }, + { + "id": 3, + "prompt": "Do the version files need updating? versions.yml already says 4.1.0.", + "expected_output": "Runs bump_versions.py --check, reports every hand-maintained literal is already 4.1.0 (no writes needed), and notes that generated artifacts are verified via bactopia-lint V001 rather than by this skill.", + "files": [] + } + ] +} diff --git a/.claude/skills/bump-versions/scripts/bump_versions.py b/.claude/skills/bump-versions/scripts/bump_versions.py new file mode 100755 index 000000000..90edf33b0 --- /dev/null +++ b/.claude/skills/bump-versions/scripts/bump_versions.py @@ -0,0 +1,158 @@ +#!/usr/bin/env python3 +"""Propagate versions.yml into Bactopia's hand-maintained version-bearing files. + +`versions.yml` at the repo root is the single, *manually edited* source of truth +for the pipeline version (`bactopia`) and the plugin pin (`nf-bactopia`). This +script only ever READS it, then copies those values into the files that carry a +literal version but are NOT regenerated by any other tool: + + conf/test_base.config bactopia_version = '...' and id 'nf-bactopia@...' + CITATION.cff version: ... + bin/bactopia VERSION=... + data/conda/meta.yaml {% set version = '...' %} + +Everything else that carries the version is a generated artifact and is left to +its regenerator: `nextflow.config` / workflow configs (bactopia-merge-schemas) +and `catalog.json` / `llms.txt` (bactopia-catalog). Those are a follow-up step, +not this script's job. + +Only the exact version token inside each match is rewritten; surrounding text is +untouched. Runs are idempotent -- a file already at the target value is reported +as "current" and left byte-for-byte unchanged. This script NEVER writes +versions.yml. +""" + +import argparse +import re +import sys +from pathlib import Path + +DEFAULT_BP = "/home/rpetit3/repos/bactopia/bactopia" + +# Each rule: (regex with three groups (prefix, version, suffix), versions.yml key, +# human label). The version token is group 2; prefix/suffix are preserved verbatim. +TARGETS: dict[str, list[tuple[str, str, str]]] = { + "conf/test_base.config": [ + (r"(bactopia_version\s*=\s*')([^']+)(')", "bactopia", "bactopia_version"), + (r"(id\s+'nf-bactopia@)([^']+)(')", "nf-bactopia", "nf-bactopia pin"), + ], + "CITATION.cff": [ + (r"(?m)(^version:[ \t]*)(\S+)()", "bactopia", "version"), + ], + "bin/bactopia": [ + (r"(?m)(^VERSION=)(\S+)()", "bactopia", "VERSION"), + ], + "data/conda/meta.yaml": [ + (r"(\{%\s*set version\s*=\s*')([^']+)(')", "bactopia", "set version"), + ], +} + + +def read_versions(bp: Path) -> dict[str, str]: + """Parse versions.yml (simple `key: value`; stdlib only). Never modified.""" + path = bp / "versions.yml" + text = path.read_text() + out: dict[str, str] = {} + for line in text.splitlines(): + m = re.match(r"([\w-]+):\s*(\S+)", line) + if m: + out[m.group(1)] = m.group(2) + for key in ("bactopia", "nf-bactopia"): + if key not in out: + raise KeyError(f"versions.yml missing required key '{key}'") + return out + + +def apply_file( + bp: Path, rel: str, rules: list[tuple[str, str, str]], versions: dict, check: bool +) -> list[dict]: + """Return a list of change records for one file; write in place unless check.""" + path = bp / rel + changes: list[dict] = [] + if not path.exists(): + return [{"file": rel, "label": "-", "status": "missing"}] + text = path.read_text() + new_text = text + for pattern, key, label in rules: + want = versions[key] + rec = {"file": rel, "label": label, "want": want} + m = re.search(pattern, new_text) + if not m: + rec["status"] = "pattern-not-found" + changes.append(rec) + continue + old = m.group(2) + rec["old"] = old + if old == want: + rec["status"] = "current" + else: + rec["status"] = "update" + new_text = ( + new_text[: m.start(2)] + want + new_text[m.end(2) :] + ) + changes.append(rec) + if not check and new_text != text: + path.write_text(new_text) + return changes + + +def main() -> int: + ap = argparse.ArgumentParser( + description="Propagate versions.yml into hand-maintained version files." + ) + ap.add_argument("--bactopia-path", default=DEFAULT_BP) + ap.add_argument( + "--check", + action="store_true", + help="dry run: report what would change, write nothing", + ) + args = ap.parse_args() + bp = Path(args.bactopia_path) + + try: + versions = read_versions(bp) + except (FileNotFoundError, KeyError) as e: + print(f"ERROR: {e}", file=sys.stderr) + return 1 + + mode = "DRY RUN (no files written)" if args.check else "APPLY" + print(f"[bump-versions] {mode}") + print( + f" source versions.yml -> bactopia={versions['bactopia']}, " + f"nf-bactopia={versions['nf-bactopia']}\n" + ) + + updated = missing = notfound = 0 + for rel, rules in TARGETS.items(): + for rec in apply_file(bp, rel, rules, versions, args.check): + s = rec["status"] + if s == "update": + verb = "would update" if args.check else "updated" + print(f" [{verb}] {rel}: {rec['label']} {rec['old']} -> {rec['want']}") + updated += 1 + elif s == "current": + print(f" [ok] {rel}: {rec['label']} already {rec['want']}") + elif s == "missing": + print(f" [WARN] {rel}: file not found") + missing += 1 + elif s == "pattern-not-found": + print(f" [WARN] {rel}: could not locate {rec['label']} literal") + notfound += 1 + + print( + f"\n[bump-versions] {'would update' if args.check else 'updated'} " + f"{updated} value(s); warnings: {missing + notfound}" + ) + if updated and not args.check: + print( + "\nNext steps (regenerated artifacts are NOT touched here):\n" + " 1. /merge-schemas all (nextflow.config + schemas from versions.yml)\n" + " 2. /update-catalog (catalog.json + llms.txt)\n" + " 3. verify: bactopia-lint repo tier -> V001/V002/V003 should pass\n" + " 4. smoke-test a module whose test container tag changed." + ) + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/.claude/skills/release-checklist/SKILL.md b/.claude/skills/release-checklist/SKILL.md new file mode 100644 index 000000000..a41fe1069 --- /dev/null +++ b/.claude/skills/release-checklist/SKILL.md @@ -0,0 +1,247 @@ +--- +name: release-checklist +description: Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report. Read-only — never commits, pushes, tags, edits issues, or regenerates tracked files. Use this whenever the user asks about release readiness, cutting a release, a release checklist, whether we can ship/tag a new version, pre-release audit, or "are we ready to release" — even if they don't say the word "checklist". Covers version consistency across bactopia/bactopia-py/nf-bactopia, nf-bactopia plugin pin + template drift, module tool-version bumps, workflow config/schema and catalog freshness, docs/citations/GroovyDoc/lint validators, recent test-run status, CHANGELOG completeness, and open-issue triage. +--- + +# Release Checklist + +Audit whether Bactopia is ready to cut a version release and produce a recommendation report. This is a **multi-repo, audit-only** skill: it reads `bactopia`, `bactopia-py`, `nf-bactopia`, and the docs-site `bactopia.github.io` (published at https://bactopia.io), plus GitHub issues, and synthesizes a GO / NO-GO report. + +## Hard constraints — read first + +- **Audit-only. Never mutate anything.** No `git commit`/`push`/`tag`, no `gh issue edit`/`comment`/`close`, no edits to any tracked source file, no running the config/catalog/schema *regenerators* against the repo. The only write is the report file under `logs/` and scratch files under a `mktemp` dir. +- **Every regeneration check writes to a temp dir and diffs** — it never overwrites tracked `nextflow.config` / `nextflow_schema.json` / `catalog.json` / `llms.txt`. +- **Report, don't fix.** When a check finds drift, record it and recommend the follow-up skill (e.g. `/update-catalog`, `/merge-schemas`, `/update-module`). Do not apply the fix here. + +## Version model (why the checks look where they do) + +The Bactopia pipeline version and the `nf-bactopia` plugin pin are **declared in `versions.yml` at the pipeline repo root** (keys `bactopia:` and `nf-bactopia:`). `bactopia-merge-schemas` reads them and renders every workflow's `nextflow.config` from the bactopia-py template, and `bactopia-catalog` reads them for `catalog.json`, so the main repo's `nextflow.config` and `catalog.json` versions are **generated artifacts**. `versions.yml` is the version source of truth; bactopia-lint's repo rules (V001/V002/V003) enforce that every version-bearing file, the CHANGELOG heading, and the plugin pin agree with it. `CITATION.cff`, `bin/bactopia`, and `data/conda/meta.yaml` carry hand-maintained literals that must be bumped to match and are frequent laggards. + +## Preamble + +Resolve paths and a timestamp (from the bash tool): + +``` +BP=/home/rpetit3/repos/bactopia/bactopia +PY=$BP/../bactopia-py +NFB=$BP/../nf-bactopia +DOCS=$BP/../bactopia.github.io +TS=$(date +%Y%m%d_%H%M%S) +AUDIT=$(mktemp -d) # scratch dir for read-only regen diffs +``` + +If a sibling repo path does not exist, run its checks in "skipped (repo not found)" mode and note it — never error out. + +## Run the checks + +Present each result; never fix. Numbers below are the report's check IDs. + +### 1. Version consistency (delegated to bactopia-lint) + +Version-bearing file consistency is enforced by bactopia-lint's **repo rules**, not re-implemented in this skill. Run bactopia-lint once — the same run feeds checks 8 and 11 — and read the `repo`-tier results: + +``` +bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path $BP --json --silent +``` + +Parse the `repo` component's `results[]` for rule IDs starting with `V`: +- **V001** (FAIL): a version-bearing file disagrees with `versions.yml` — `nextflow.config`, `catalog.json`, `bin/bactopia`, `data/conda/meta.yaml`, `CITATION.cff`, or any `*.config` `bactopia_version` / `nf-bactopia@` pin. Module/subworkflow test configs inherit both from `conf/test_base.config`, so that single file is the usual test-side offender (not the ~180 individual test configs). The message groups offenders by value. +- **V002** (FAIL): `versions.yml: bactopia` ≠ the top `## vX.Y.Z` CHANGELOG heading (disagreement on what's being released). +- Passing rules are **not** listed individually (PASS components have empty `results[]`); absence of a V-FAIL means clean. +- Any V001/V002 FAIL ⇒ **check 1 = FAIL**. Fixes: regenerate configs (`/merge-schemas` + `/update-catalog`), hand-bump `CITATION.cff` / `bin/bactopia` / `data/conda/meta.yaml`, and bump `bactopia_version` in `conf/test_base.config` (the single source for every module/subworkflow test config). +- **Staleness guard:** the lint JSON MUST contain a `repo` component. If it does not, bactopia-py predates the version rules and the core version gate could not run — this is a **FAIL** (never a false PASS): report "version rules V001–V003 not loaded; update bactopia-py" and treat the release as NO-GO until re-audited with current tooling. + +The deterministic engine is run once and feeds checks 2, 12, 13: + +``` +python3 .claude/skills/release-checklist/scripts/release_audit.py --bactopia-path $BP --json +``` + +It returns `sibling_release_state` (check 12), `changelog` (check 13), `module_updates` (check 2), and `warnings[]` — surface any warnings. + +### 2. Module tool versions (offline — reads the /update-module record) + +This check does **not** hit the network. `bactopia-update` queries the Anaconda API for ~100 modules (~2 min), so the audit never runs it — instead it reads the record that `/update-module` leaves under `logs/module-updates/.json`. The engine's `module_updates` field carries the result: + +- `present: false` ⇒ **FAIL (blocking → NO-GO)**: no module-version check is on record for this cycle. Recommend: run `/update-module` (which writes the record) and then re-run `/run-tests`, before re-auditing. This is a hard release gate — do not hand-wave it. +- `present: true`: + - `module_config_changed_after: true` ⇒ **WARN**: `module.config` files changed after the record was written, so it is stale — re-run `/update-module`. + - `needs_update > 0` ⇒ **WARN**: that many modules have newer tool versions available — run `/update-module` to apply them. + - otherwise ⇒ **PASS**: module versions were checked at `log_timestamp`; the `needs_user_review` count is informational (multi-package modules needing manual review). + +Report `log_timestamp`, `needs_update`, `needs_user_review`, and `up_to_date` from the record. Never edit configs and never call `bactopia-update` from this skill. + +### 3. Workflow config/schema freshness (read-only diff) + +For each of the 4 named workflows — `bactopia`, `teton`, `staphopia`, `cleanyerreads` (paths from `catalog.json.workflows[].path`) — regenerate into the scratch dir and diff against the committed copies: + +``` +bash .claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \ + --bactopia-path $BP --wf --outdir $AUDIT/ +diff $AUDIT//nextflow.config +diff $AUDIT//nextflow_schema.json +``` + +The scratch dir is empty, so `--force` is not needed and nothing tracked is touched. Any diff ⇒ the committed file is stale relative to current module schemas/template ⇒ recommend `/merge-schemas`. The root `bactopia` config round-trips cleanly, so a root diff usually means a module was added/removed without rewiring, or the template version was bumped without regenerating. Only extend to the ~66 bactopia-tools if the user explicitly asks ("all tools") — tool schemas are otherwise covered by their nf-tests. + +### 4. Catalog & llms.txt freshness (read-only diff) + +``` +bash .claude/skills/update-catalog/scripts/run-bactopia-catalog.sh \ + --bactopia-path $BP --output $AUDIT/catalog.json --pretty --llms-output $AUDIT/llms.txt +diff $AUDIT/catalog.json $BP/catalog.json +diff $AUDIT/llms.txt $BP/llms.txt +``` + +Any diff ⇒ stale ⇒ recommend `/update-catalog`. + +### 5. Docs-site (bactopia.io) version state + +In `$DOCS` (skip with a note if the repo is absent): + +- **(a) version label** — read `versions.current.label` in `docusaurus.config.ts`; compare to the release target. A lagging label is a WARN ("bump on release"). +- **(b) changelog mirror** — compare the top `## v` heading of `docs/changelog.md` to the main repo `CHANGELOG.md` top heading. A version mismatch is a WARN (mirror out of sync). +- **(c) plugin pins** — V001 only scans the bactopia repo's `*.config` files, so the docs site is not covered by the linter. Grep it directly: `grep -rn 'nf-bactopia@' "$DOCS" --include='*.md' --include='*.mdx'` and flag any pin that lags `versions.yml: nf-bactopia` (currently `developers/nf-bactopia/index.mdx` pins `2.0.3`). WARN. + +### 6. Docs sync (.claude/docs) + +``` +bash .claude/skills/review-docs/scripts/run-bactopia-docs.sh --bactopia-path $BP --validate --json --silent +``` + +Record `summary.fail`. Any FAIL ⇒ recommend `/review-docs`. + +### 7. Citations integrity + +``` +bash .claude/skills/review-citations/scripts/run-bactopia-citations.sh --bactopia-path $BP --validate --json --silent +``` + +Record `summary.orphans_total` and `summary.missing_total`. Either > 0 ⇒ recommend `/review-citations`. (`expected_orphans` are informational, not failures.) + +### 8. GroovyDoc / lint + +Reuse the bactopia-lint run from check 1 (do not run it twice). Count **component** FAIL results — module (`M0xx`/`MC0xx`), subworkflow (`S0xx`), workflow (`W0xx`) — and **exclude the `repo`-tier `V0xx` rules**, which are reported under checks 1 and 11. Any component FAIL ⇒ recommend `/review-groovydoc`. + +### 9. Python lint (bactopia-py) + +Run the configured ruff linter in `$PY` (prefer the justfile recipe, fall back to ruff directly): + +``` +cd $PY && just lint # == poetry run ruff check . ; fallback: ruff check . +``` + +Interpret the exit: lint findings (ruff reports violations) ⇒ **FAIL** recommending a ruff pass in bactopia-py. But distinguish "linter unavailable" from "lint failed": if neither `just` nor `ruff` is installed/resolvable in `$PY` (command-not-found, or `just lint` errors because the poetry env isn't set up), report **SKIP** ("ruff not available in this environment"), never FAIL — a missing tool is not a release blocker. + +### 10. Test-run freshness (never launches a run) + +Test runs live under `logs/run-tests//` (written by `/run-tests`); `bactopia-review-tests` defaults to the newest one. An aborted run leaves a dir with **no `summary.json`** and the CLI errors on it, so pick the newest run dir that actually has a summary and review it explicitly: + +``` +LATEST_RUN=$(for d in $(ls -1dt "$BP"/logs/run-tests/[0-9]*/ 2>/dev/null); do [ -f "$d/summary.json" ] && basename "$d" && break; done) +bash .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path $BP --run "$LATEST_RUN" --silent +``` + +Also count how many `logs/run-tests/[0-9]*/` dirs are newer than `$LATEST_RUN` but lack a `summary.json` — those are incomplete/aborted runs worth flagging. + +Relay the reviewed run's pass/fail status. Then judge **staleness**: compare `$LATEST_RUN`'s timestamp to the newest tracked-source commit (`git -C $BP log -1 --format=%ct`) and the working-tree dirty state (`sibling_release_state.bactopia.dirty_files` from the engine). Report `stale` if code changed after the run or the tree is dirty. Severity: a failing reviewed run ⇒ **FAIL**; a passing-but-stale run, or the presence of newer incomplete run dirs, ⇒ **WARN** recommending `/run-tests`; if no run dir has a `summary.json` at all ⇒ **WARN** ("no completed test run on record"). Never trigger a run from this skill. + +### 11. nf-bactopia plugin currency (bactopia-lint V003) + +From the same lint run, read repo rule **V003**: `versions.yml: nf-bactopia` vs the nf-bactopia repo's `build.gradle` latest. A `WARN` means the declared pin lags the newest nf-bactopia release — surface it; adopting the newer plugin may be intentional, so it's a judgment call, not a hard block. PASS/absent = current. Per-config pin drift is already covered by V001 (check 1). If the nf-bactopia repo isn't checked out, V003 PASSes with a "cannot verify" note. + +### 12. Sibling repo release state + +From the engine's `sibling_release_state`: per repo (`bactopia`, `bactopia-py`, `nf-bactopia`) report `latest_tag`, `commits_ahead`, `dirty_files`, `changelog_top`, `needs_release`. Flag each repo with `needs_release: true` (WARN) — unreleased commits past its last tag mean it may need its own release before the pipeline release. + +### 13. CHANGELOG completeness & concision + +Model-judgment check using the engine's `changelog` data: + +- `placeholder: true` (codename `"???"` or a `?` in the date) ⇒ **FAIL** (fill codename + date before release). +- `missing_section_for_target: true` ⇒ **FAIL** (the declared `target_version` from `versions.yml` has no `## v` CHANGELOG section at all). Whether the top heading equals the target is V002's job (check 1). +- Concision: the last git tag can predate multiple unreleased versions, so `commits_since_tag` may legitimately exceed `top_section_bullets` — do **not** treat that as an equality target. WARN only if top-section bullets are multi-sentence/verbose relative to peers, or the coverage gap looks like genuinely missing entries. Keep it qualitative; no bullet cap. + +### 14. Open-issue triage + +``` +gh issue list --repo bactopia/bactopia --state open --limit 300 \ + --json number,title,labels,updatedAt +``` + +- Exclude issues whose labels include the ignore label — default `release-ignore`, or whatever label the user names. If the label doesn't exist in the repo, nothing is filtered (no error). Report how many were excluded. +- Report total open, the excluded count, and a breakdown by label. +- Surface a **shortlist (≤10)** of likely release-relevant issues: labeled `bug`, referenced by `#` in the top CHANGELOG section, or updated within ~30 days. For each, give a one-line **address / postpone** suggestion. +- This check is **INFO** — it never changes the overall verdict on its own. Never edit, label, or comment on issues. + +### 15. Version-pinned datasets published + +`bactopia datasets` downloads pre-compiled bundles from `https://datasets.bactopia.com/datasets/v/`, where `` is the pipeline version from `versions.yml`. On a release the version is bumped **before** that version's bundle is uploaded, so the URL 404s and every dataset-dependent run — and the `bactopia_datasets` nf-test — fails. Probe the target version's bundle (read-only HEAD; the audit never uploads): + +``` +V=$(awk '/^bactopia:/{print $2}' $BP/versions.yml) +curl -s -o /dev/null -w '%{http_code}' -I "https://datasets.bactopia.com/datasets/v${V}/amrfinderplus.tar.gz" +``` + +- HTTP `200` ⇒ **PASS**: the v`` datasets are published. +- Anything else (typically `404`) ⇒ **FAIL (blocking → NO-GO)**: the v`` dataset bundle is not published. Publishing the versioned datasets is a required release step; until it lands, `bactopia datasets` 404s for users and the `bactopia_datasets` tests fail. The version-pinned `amrfinderplus.tar.gz` is a sufficient sentinel (other bundles like `mash-refseq88...` are not version-gated). **Fix:** run `/update-datasets` to rebuild `amrfinderplus.tar.gz` in the pinned container and publish it to `bactopia-r2:bactopia/datasets/v/`. + +## Synthesize the report (the primary deliverable) + +The report is produced two ways from the same content: + +1. **Write the full report** to `$BP/logs/release-audit-$TS.md` using the template below (all 15 checks, Blocking / Non-blocking sections, and a Details section per check with findings + the recommended follow-up skill). `logs/` is the scratch/output dir; use a single timestamped **file** (not a `logs//` dir) so `/review-tests`' run-dir scan ignores it. If `logs/` is unwritable, fall back to `$AUDIT/release-audit-$TS.md` and report that path. +2. **Present a condensed view in chat**: the Overall verdict line, the Checklist table, and the Blocking-items list — then end with the saved path, e.g. `Full report saved to: /home/rpetit3/repos/bactopia/bactopia/logs/release-audit-.md`. + +### Report template + +``` +# Bactopia Release Readiness Audit — +**Target release:** v **Overall: ** + + + +## Checklist +| # | Check | Status | Summary | +|---|-------|--------|---------| +| 1 | Version consistency | | ... | +| 2 | Module tool versions | ... | ... | +| 3 | Workflow configs & schemas | ... | ... | +| 4 | Catalog & llms.txt freshness | ... | ... | +| 5 | Docs-site (bactopia.io) state| ... | ... | +| 6 | Docs sync (.claude/docs) | ... | ... | +| 7 | Citations | ... | ... | +| 8 | GroovyDoc / lint | ... | ... | +| 9 | Python lint (ruff) | ... | ... | +| 10 | Test-run freshness | ... | ... | +| 11 | nf-bactopia plugin currency | ... | ... | +| 12 | Sibling repo release state | ... | ... | +| 13 | CHANGELOG completeness | ... | ... | +| 14 | Open issues | INFO | | +| 15 | Version-pinned datasets | | | + +## Blocking items (must fix before release) +- ... + +## Non-blocking / judgment items +- ... + +## Details +### 1. Version consistency (bactopia-lint V001/V002) + conf/test_base.config + CITATION.cff/bin/bactopia/meta.yaml), then regenerate generated artifacts with /merge-schemas + /update-catalog> +### 2. Module tool versions +... +``` + +### Severity + overall verdict (deterministic — status is never a guess) + +- **FAIL (blocking)**: check 1 — bactopia-lint **V001** (a version-bearing file ≠ `versions.yml`) or **V002** (`versions.yml` ≠ CHANGELOG top heading) reports FAIL, **or** the lint `repo` component is absent (version rules not loaded); CHANGELOG `placeholder` or `missing_section_for_target` (check 13); **no `/update-module` record — `module_updates.present == false` (check 2)**; schema/config drift (check 3); catalog/llms drift (check 4); any component docs/citations/lint failure (checks 6–8); a ruff lint failure when ruff is available (check 9); a failing test run (check 10); **the target-version dataset bundle is unpublished — `datasets.bactopia.com/datasets/v/` 404s (check 15)**. +- **WARN (non-blocking / judgment)**: pending module updates or a stale `/update-module` record (check 2); the declared nf-bactopia pin lags latest — V003 (check 11); a sibling repo with `needs_release` (check 12); docs-site label or changelog-mirror lag (checks 5a/5b); a passing-but-stale test run (check 10); a CHANGELOG concision concern (check 13). +- **PASS / SKIP / INFO**: PASS = check clean; SKIP = a check that could not run (e.g. ruff not installed, check 9) — never a blocker; INFO = informational only (check 14). None of these force a caveat. +- **Overall** = `NO-GO` if any FAIL; `GO WITH CAVEATS` if only WARN; `GO` if all PASS. Open issues (check 14) are INFO and never change the overall verdict on their own. + +## Notes + +- All `run-bactopia-*.sh` wrappers auto-discover their CLI (PATH → `bactopia-dev` conda env → `bactopia-py` → any `bactopia-*` env), so no env activation is needed. +- `--bactopia-path` is always `/home/rpetit3/repos/bactopia/bactopia`. +- The engine (`release_audit.py`) needs only `git` + the Python stdlib; it does not use conda or any `bactopia-*` CLI. diff --git a/.claude/skills/release-checklist/evals/evals.json b/.claude/skills/release-checklist/evals/evals.json new file mode 100644 index 000000000..141256520 --- /dev/null +++ b/.claude/skills/release-checklist/evals/evals.json @@ -0,0 +1,44 @@ +{ + "skill_name": "release-checklist", + "evals": [ + { + "id": 1, + "prompt": "are we ready to cut the v4.1.0 release? give me a go/no-go", + "expected_output": "A release-readiness report saved to logs/release-audit-.md and summarized in chat with an explicit GO / GO WITH CAVEATS / NO-GO verdict. Version consistency is sourced from bactopia-lint's repo rules (V001/V002), not re-derived in the skill; any version drift is reported via the failing V-rule. The audit makes no writes to tracked source or GitHub.", + "files": [], + "assertions": [ + "delegates_version_to_lint: check 1 (version consistency) is sourced from bactopia-lint repo rules V001/V002, not a re-implemented scan", + "reports_version_drift_from_vrule: if version-bearing files disagree with versions.yml, the report cites the V001 (or V002) finding rather than inventing its own", + "emits_overall_verdict: the report contains an explicit GO / GO WITH CAVEATS / NO-GO verdict", + "saves_markdown_report: a report file is written under logs/ (release-audit-.md) and its path is surfaced to the user", + "read_only: no git commit/push/tag, no gh issue edit/comment/close, and no edits to tracked source files" + ] + }, + { + "id": 2, + "prompt": "run the release checklist and tell me what's blocking a release", + "expected_output": "The full 14-check audit report plus a condensed chat summary (verdict + checklist table + blocking list). Version/pin checks are attributed to bactopia-lint V001/V002/V003; the module tool-version check reads the offline /update-module record (no network); blocking (FAIL) items are separated from non-blocking (WARN) items.", + "files": [], + "assertions": [ + "runs_all_checks: the report includes all 14 checklist rows with per-check status", + "version_check_via_lint: version and nf-bactopia pin findings are attributed to bactopia-lint (V001/V002/V003), not to a bespoke engine scan", + "module_versions_offline: check 2 reads the /update-module record (present/absent, log timestamp) and does not query the Anaconda API", + "separates_blocking_from_nonblocking: FAIL items are listed as blocking; WARN items as non-blocking/judgment", + "read_only: no git commit/push/tag, no gh mutation, no edits to tracked source files" + ] + }, + { + "id": 3, + "prompt": "do a pre-release audit across bactopia, bactopia-py, and nf-bactopia", + "expected_output": "A multi-repo audit report covering all three repos plus the docs site (bactopia.io), saved to logs/ and summarized in chat, including per-repo release state (latest tag, commits ahead, dirty files) from the engine and an open-issue summary that honors the release-ignore label.", + "files": [], + "assertions": [ + "covers_all_repos: the report addresses bactopia, bactopia-py, nf-bactopia, and the docs site (bactopia.io)", + "reports_sibling_release_state: per-repo latest tag and commits-ahead are reported (from the engine's sibling_release_state)", + "includes_issue_summary: the report includes an open-issue count and a shortlist, and mentions the release-ignore ignore label plus the excluded count", + "emits_overall_verdict: the report contains an explicit GO / GO WITH CAVEATS / NO-GO verdict", + "read_only: no git commit/push/tag, no gh mutation, no edits to tracked source files" + ] + } + ] +} diff --git a/.claude/skills/release-checklist/scripts/release_audit.py b/.claude/skills/release-checklist/scripts/release_audit.py new file mode 100755 index 000000000..6b5da5e5c --- /dev/null +++ b/.claude/skills/release-checklist/scripts/release_audit.py @@ -0,0 +1,284 @@ +#!/usr/bin/env python3 +"""Deterministic release-readiness checks for Bactopia (audit-only). + +Covers the git + file-state checks that are NOT version-file consistency: +sibling-repo release state, CHANGELOG structure, and the /update-module record. +It never writes to any repo and never touches git history -- `git` is invoked +read-only (describe/tag/rev-list/status/log). + +Version-bearing file consistency (versions.yml vs nextflow.config, catalog.json, +CITATION.cff, bin/bactopia, data/conda/meta.yaml, every *.config bactopia_version +and nf-bactopia@ pin, versions.yml vs CHANGELOG, and the declared nf-bactopia pin +vs the nf-bactopia repo's latest) is owned by the `bactopia-lint` repo rules +V001/V002/V003 -- the release-checklist skill surfaces those from the lint run +rather than re-implementing them here. + +Companion to the `release-checklist` skill: the SKILL.md orchestrates the +CLI-backed checks (bactopia-lint/update/merge-schemas/catalog/docs/citations/ +review-tests) and gh; this script owns the remaining pure file+git checks. +""" + +import argparse +import json +import re +import subprocess +import sys +from datetime import datetime, timezone +from pathlib import Path + +_SECTION_RE = re.compile(r"^##\s+v?(\d+\.\d+\.\d+)\b") + + +# --------------------------------------------------------------------------- # +# small helpers +# --------------------------------------------------------------------------- # +def _read(path: Path) -> str | None: + try: + return path.read_text(encoding="utf-8", errors="replace") + except OSError: + return None + + +def _git(repo: Path, *args: str) -> str | None: + """Run a read-only git command in `repo`; return stripped stdout or None.""" + try: + out = subprocess.run( + ["git", "-C", str(repo), *args], + capture_output=True, text=True, timeout=30, + ) + except (OSError, subprocess.SubprocessError): + return None + if out.returncode != 0: + return None + return out.stdout.strip() + + +def _changelog_top(text: str | None) -> dict: + """Parse the top `## v ... "codename" date` heading of a CHANGELOG.""" + result = {"version": None, "codename": None, "date": None, "placeholder": False} + if not text: + return result + for line in text.splitlines(): + m = _SECTION_RE.match(line) + if not m: + continue + result["version"] = m.group(1) + cm = re.search(r'"([^"]*)"', line) + if cm: + result["codename"] = cm.group(1) + dm = re.search(r'"[^"]*"\s*[-\s]*(.+?)\s*$', line) + if dm: + result["date"] = dm.group(1).strip() + cn = result["codename"] + dt = result["date"] or "" + result["placeholder"] = (cn is not None and "?" in cn) or ("?" in dt) + break + return result + + +def _all_sections(text: str | None) -> list[str]: + if not text: + return [] + return [m.group(1) for line in text.splitlines() + if (m := _SECTION_RE.match(line))] + + +def _read_versions_yml(bp: Path) -> dict: + """Parse the declared versions.yml (simple `key: value`; stdlib only).""" + text = _read(bp / "versions.yml") + out = {"present": text is not None, "bactopia": None, "nf_bactopia": None} + if not text: + return out + for line in text.splitlines(): + m = re.match(r"\s*([A-Za-z0-9_-]+)\s*:\s*(\S+)", line) + if not m: + continue + key, val = m.group(1), m.group(2).strip().strip("'\"") + if key == "bactopia": + out["bactopia"] = val + elif key in ("nf-bactopia", "nf_bactopia"): + out["nf_bactopia"] = val + return out + + +# --------------------------------------------------------------------------- # +# check families +# --------------------------------------------------------------------------- # +def sibling_release_state(repos: dict[str, Path | None], warnings: list) -> dict: + out = {} + for name, repo in repos.items(): + if not repo or not repo.exists(): + out[name] = None + warnings.append(f"repo '{name}' not found; release-state skipped") + continue + latest_tag = _git(repo, "describe", "--tags", "--abbrev=0") + commits_ahead = None + if latest_tag: + cnt = _git(repo, "rev-list", f"{latest_tag}..HEAD", "--count") + commits_ahead = int(cnt) if cnt and cnt.isdigit() else None + status = _git(repo, "status", "--porcelain") + dirty = len([ln for ln in status.splitlines() if ln.strip()]) if status else 0 + changelog = _changelog_top(_read(repo / "CHANGELOG.md")) + out[name] = { + "latest_tag": latest_tag, + "commits_ahead": commits_ahead, + "dirty_files": dirty, + "changelog_top": changelog["version"], + "needs_release": bool(commits_ahead and commits_ahead > 0), + } + return out + + +def changelog_state(bp: Path) -> dict: + text = _read(bp / "CHANGELOG.md") + sections = _all_sections(text) + top = _changelog_top(text) + latest_tag = _git(bp, "describe", "--tags", "--abbrev=0") + commits_since_tag = None + if latest_tag: + log = _git(bp, "log", f"{latest_tag}..HEAD", "--oneline") + commits_since_tag = len(log.splitlines()) if log else 0 + # bullets in the top section (until the next `## ` heading) + top_bullets = 0 + if text: + in_top = False + for line in text.splitlines(): + if _SECTION_RE.match(line): + if in_top: + break + in_top = True + continue + if in_top and re.match(r"^\s*-\s+", line): + top_bullets += 1 + # release target = declared version (versions.yml); it must have a section + target = _read_versions_yml(bp).get("bactopia") + missing = bool(target and target not in sections) + return { + "target_version": target, + "top_version": top["version"], + "codename": top["codename"], + "date": top["date"], + "placeholder": top["placeholder"], + "latest_tag": latest_tag, + "sections": sections, + "commits_since_tag": commits_since_tag, + "top_section_bullets": top_bullets, + "missing_section_for_target": missing, + } + + +def module_updates(bp: Path) -> dict: + """Read the newest /update-module record under logs/module-updates/. + + The update-module skill writes bactopia-update's JSON there after each run. + This is offline -- it only reads the record, never queries the network. + Returns present=False when no record exists (a release blocker). + """ + log_dir = bp / "logs" / "module-updates" + files = sorted(log_dir.glob("*.json")) if log_dir.is_dir() else [] + if not files: + return {"present": False, "log_dir": str(log_dir)} + newest = files[-1] # timestamped filenames sort chronologically + m = re.match(r"(\d{8}_\d{6})", newest.stem) + log_ts = None + if m: + try: + log_ts = int(datetime.strptime(m.group(1), "%Y%m%d_%H%M%S") + .replace(tzinfo=timezone.utc).timestamp()) + except ValueError: + log_ts = None + if log_ts is None: + try: + log_ts = int(newest.stat().st_mtime) + except OSError: + log_ts = None + + needs_update = needs_review = up_to_date = total = None + try: + data = json.loads(newest.read_text()) + rows = data.get("results", data) if isinstance(data, dict) else data + if isinstance(rows, dict): + rows = rows.get("modules") or rows.get("results") or [] + if isinstance(rows, list): + rows = [x for x in rows if isinstance(x, dict) + and not (x.get("tool") == "aria2" + and x.get("module") == "checkm2_download")] + total = len(rows) + needs_update = sum(1 for x in rows if x.get("needs_update")) + needs_review = sum(1 for x in rows if x.get("needs_user_review")) + up_to_date = total - needs_update - needs_review + except (OSError, json.JSONDecodeError): + pass + + cfg_ts = _git(bp, "log", "-1", "--format=%ct", + "--", ":(glob)modules/**/module.config") + cfg_ts = int(cfg_ts) if cfg_ts and cfg_ts.isdigit() else None + return { + "present": True, + "log_file": str(newest), + "log_timestamp": m.group(1) if m else newest.stem, + "needs_update": needs_update, + "needs_user_review": needs_review, + "up_to_date": up_to_date, + "total": total, + "module_config_changed_after": bool(log_ts and cfg_ts and cfg_ts > log_ts), + } + + +# --------------------------------------------------------------------------- # +# entry point +# --------------------------------------------------------------------------- # +def _resolve(explicit: str | None, default: Path) -> Path | None: + path = Path(explicit) if explicit else default + return path if path.exists() else None + + +def main() -> int: + ap = argparse.ArgumentParser(description="Deterministic Bactopia release audit.") + ap.add_argument("--bactopia-path", required=True) + ap.add_argument("--bactopia-py-path") + ap.add_argument("--nf-bactopia-path") + ap.add_argument("--docs-site-path") + ap.add_argument("--json", action="store_true", + help="emit JSON (default; kept for parity with other CLIs)") + args = ap.parse_args() + + bp = Path(args.bactopia_path).resolve() + if not bp.exists(): + print(json.dumps({"error": f"bactopia-path not found: {bp}"})) + return 0 + parent = bp.parent + py = _resolve(args.bactopia_py_path, parent / "bactopia-py") + nfb = _resolve(args.nf_bactopia_path, parent / "nf-bactopia") + docs = _resolve(args.docs_site_path, parent / "bactopia.github.io") + + warnings: list[str] = [] + for name, path in (("bactopia-py", py), ("nf-bactopia", nfb), + ("bactopia.github.io", docs)): + if path is None: + warnings.append(f"sibling repo '{name}' not found near {parent}") + + siblings = sibling_release_state( + {"bactopia": bp, "bactopia-py": py, "nf-bactopia": nfb}, warnings) + cl = changelog_state(bp) + mu = module_updates(bp) + + report = { + "bactopia_path": str(bp), + "paths": { + "bactopia_py": str(py) if py else None, + "nf_bactopia": str(nfb) if nfb else None, + "docs_site": str(docs) if docs else None, + }, + "sibling_release_state": siblings, + "changelog": cl, + "module_updates": mu, + "warnings": warnings, + "generated": datetime.now(timezone.utc).isoformat(), + } + print(json.dumps(report, indent=2)) + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/.claude/skills/review-tests/SKILL.md b/.claude/skills/review-tests/SKILL.md index d65bcd8f7..e0ebc585e 100644 --- a/.claude/skills/review-tests/SKILL.md +++ b/.claude/skills/review-tests/SKILL.md @@ -56,15 +56,15 @@ Run the review-tests CLI and present the results to the user. The initial summary should be compact and scannable. When the user asks for deeper detail: - **Specific component**: Read its stdout file at - `logs/{timestamp}/{tier}/{component}.stdout.txt` using the Read tool + `logs/run-tests/{timestamp}/{tier}/{component}.stdout.txt` using the Read tool - **Undeclared outputs**: Read the component's `.outputs.txt` file at - `logs/{timestamp}/{tier}/{component}.outputs.txt` for the full file list. + `logs/run-tests/{timestamp}/{tier}/{component}.outputs.txt` for the full file list. Then read the module's `main.nf` to see the current `results` and `logs` fields and advise where each undeclared file should go. - **Abort errors**: Read the nextflow.log for the component (focus on ERROR/WARN lines and last 50 lines). To find the log path, re-run with `--json` and check the `nextflow_log` field, - or look in `logs/{timestamp}/{tier}/{component}.stdout.txt` for the path. + or look in `logs/run-tests/{timestamp}/{tier}/{component}.stdout.txt` for the path. - **Assertion details**: Read the stdout file and look for specific assertion mismatch information @@ -78,7 +78,7 @@ Do NOT read nextflow.log or stdout files during the initial summary. assertion failures -- snapshots were already regenerated during this run. These represent non-deterministic output or incorrect test assertions. - Always read `.stdout.txt` files for diagnostics, NOT `.stderr.txt` -- The `logs/{timestamp}/` directory contains tier subdirectories based on what +- The `logs/run-tests/{timestamp}/` directory contains tier subdirectories based on what was tested -- not all tiers are present in every run - The `.nf-test/` work directories under component test dirs only exist for failed tests (including `undeclared_outputs` failures -- preserved for review) diff --git a/.claude/skills/run-tests/SKILL.md b/.claude/skills/run-tests/SKILL.md index 197a07085..a77af5577 100644 --- a/.claude/skills/run-tests/SKILL.md +++ b/.claude/skills/run-tests/SKILL.md @@ -8,7 +8,7 @@ description: Run Bactopia nf-tests via bactopia-test and produce a timestamped l Run the Bactopia nf-test suite through `bactopia-test` for a specific component and present the live output to the user. This is the "before" half of the `run-tests` / `review-tests` pair: this skill **runs** the tests and writes a -timestamped `logs/{timestamp}/` directory; `/review-tests` then **interprets** +timestamped `logs/run-tests/{timestamp}/` directory; `/review-tests` then **interprets** that directory (grouping failures, reading stdout files, etc.). Keep the two responsibilities clearly separated -- do not try to do `/review-tests`' job here. @@ -78,7 +78,7 @@ These flags are always added without asking the user: | `--test-data` | `/home/rpetit3/repos/bactopia/bactopia-tests`| Canonical test-data location; sets `BACTOPIA_TESTS`. | | `--profile` | `docker` | Default execution profile. Docker is the baseline for reproducible tests. | | `--keep` | *(always)* | Preserves `.nf-test/` dirs and logs on pass; `/review-tests` needs them. | -| `--outdir` | `/home/rpetit3/repos/bactopia/bactopia` | So `logs/{timestamp}/` lands at the repo root, where `/review-tests` reads. | +| `--outdir` | `/home/rpetit3/repos/bactopia/bactopia` | So `logs/run-tests/{timestamp}/` lands at the repo root, where `/review-tests` reads. | ## When to ask the user first (never auto-fill) @@ -111,7 +111,7 @@ time or delete work the user cares about. to read into them to diagnose undeclared outputs or assertion mismatches. - **ALWAYS pass `--outdir /home/rpetit3/repos/bactopia/bactopia`** so that - `logs/{timestamp}/` is written at the bactopia repo root. `/review-tests` + `logs/run-tests/{timestamp}/` is written at the bactopia repo root. `/review-tests` looks for logs relative to `--bactopia-path`; if `--outdir` is omitted the logs land in whatever directory the shell was invoked from and the downstream skill will not find them. @@ -145,7 +145,7 @@ When `bactopia-test` finishes, do these four things -- nothing more: 2. **Extract the run timestamp.** The CLI prints the path to the logs directory, which ends in a `YYYYMMDD_HHMMSS` directory (e.g. - `logs/20260410_143022/`). Pull that timestamp out and show it to the user. + `logs/run-tests/20260410_143022/`). Pull that timestamp out and show it to the user. 3. **Point the user at `/review-tests`** with an exact next step: @@ -225,7 +225,7 @@ Defaults in parentheses. ### Output layout written by the CLI ``` -{outdir}/logs/{YYYYMMDD_HHMMSS}/ +{outdir}/logs/run-tests/{YYYYMMDD_HHMMSS}/ ├── summary.json # machine-readable rollup ├── summary.tsv # same data in TSV ├── modules/ @@ -269,7 +269,7 @@ are forwarded through `"$@"`. ### Sibling skills -- `/review-tests` — the "after" half. Reads `logs/{timestamp}/`, groups +- `/review-tests` — the "after" half. Reads `logs/run-tests/{timestamp}/`, groups failures by type, reads stdout files on request, and suggests next steps. Always point the user here after a run completes. - `/project-status` — component counts and coverage. Unrelated to the test diff --git a/.claude/skills/update-datasets/SKILL.md b/.claude/skills/update-datasets/SKILL.md new file mode 100644 index 000000000..a3c7bce56 --- /dev/null +++ b/.claude/skills/update-datasets/SKILL.md @@ -0,0 +1,95 @@ +--- +name: update-datasets +description: Build and publish Bactopia's version-pinned datasets to Cloudflare R2. Currently implements the AMRFinder+ database: verifies the amrfinderplus module is at the latest bioconda version, rebuilds amrfinderplus.tar.gz inside the module's pinned container, and (after confirmation) uploads it via rclone to datasets/v/amrfinderplus.tar.gz. Use when asked to update datasets, rebuild the amrfinderplus database, publish a dataset bundle, refresh the version-pinned datasets, or prepare datasets for a release. +--- + +# Update Datasets + +Build and publish Bactopia's **version-pinned** datasets to Cloudflare R2. + +`bactopia datasets` downloads bundles from `https://datasets.bactopia.com/datasets/`. +Most bundles are shared across releases, but a few are pinned to the pipeline +version. The only version-pinned dataset today is **AMRFinder+** +(`conf/params.config`: `amrfinderplus_url = ".../datasets/v${params.bactopia_version}/amrfinderplus.tar.gz"`), +so this skill implements that path concretely; the name stays generic for future +version-pinned datasets. + +The publish version is `versions.yml`'s `bactopia` value, and the R2 layout is +`datasets/v/amrfinderplus.tar.gz`. The tool version that **builds** the +database must equal the version the pipeline **pins** (an outdated binary can +produce a database the pinned binary cannot load), so the skill hard-gates on +the `amrfinderplus` module being current before building. This skill is the sole +owner of the build recipe — the old `modules/amrfinderplus/update/` module that +carried it was removed. + +## Steps + +1. **Currency gate (hard stop).** Confirm the module tool is the latest bioconda + release before building: + ``` + bash .claude/skills/update-module/scripts/run-bactopia-update.sh \ + --bactopia-path /home/rpetit3/repos/bactopia/bactopia --module amrfinderplus --json --silent + ``` + Parse the entry whose `tool == "ncbi-amrfinderplus"`. + - `needs_update == true` -> **STOP**. Tell the user to run `/update-module` + (bumps `modules/amrfinderplus/run/module.config`), then re-run this skill. + Do not build against a stale version. + - `latest_version == null` (API failure) -> **STOP** and report the failure. + - `needs_update == false` -> proceed. + +2. **Build.** Rebuild the database in the module's pinned container: + ``` + bash .claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh \ + --bactopia-path /home/rpetit3/repos/bactopia/bactopia + ``` + Add `--runtime singularity` if the user asks or docker is unavailable. This + downloads the latest NCBI database and produces the tarball; expect it to take + several minutes and hundreds of MB. The script reads the container image from + `modules/amrfinderplus/run/module.config`, so version bumps flow automatically. + +3. **Report the build.** Show the script's summary fields (tarball path, sha256, + tool version, database version). Read the publish version: + ``` + awk '/^bactopia:/{print $2}' /home/rpetit3/repos/bactopia/bactopia/versions.yml + ``` + The R2 key is `datasets/v/amrfinderplus.tar.gz`. + +4. **Upload (gated behind explicit confirmation).** The rclone destination base + is `bactopia-r2:bactopia` (remote `bactopia-r2`, bucket `bactopia`); + `$BACTOPIA_R2_DEST` overrides it if set. The public URL + `https://datasets.bactopia.com/datasets/...` maps to + `bactopia-r2:bactopia/datasets/...`, so the full key is + `/datasets/v/amrfinderplus.tar.gz`. + - Verify reachability: `rclone lsd bactopia-r2:bactopia`. On failure, report + it and fall back to printing the manual command below — do not upload. + - Show the exact command and **ask for confirmation** before running it: + ``` + rclone copyto "" "bactopia-r2:bactopia/datasets/v/amrfinderplus.tar.gz" --s3-no-check-bucket --progress + ``` + - `--s3-no-check-bucket` is **required**: R2 API tokens cannot `CreateBucket`, + which rclone otherwise attempts before the first upload and fails with a + `403 AccessDenied`. The bucket already exists, so skip the check. + - Only on an explicit yes, run it. `copyto` overwrites an existing key, so + re-publishing a version is idempotent. + +5. **Verify publication.** After upload, confirm the public URL resolves: + ``` + curl -s -o /dev/null -w '%{http_code}' -I "https://datasets.bactopia.com/datasets/v/amrfinderplus.tar.gz" + ``` + `200` -> published (this is exactly `/release-checklist` check 15's sentinel). + Report the HTTP code. + +## Notes + +- The currency gate reuses `/update-module`'s `run-bactopia-update.sh`; the build + image is read from `modules/amrfinderplus/run/module.config`, so a version bump + there is picked up without editing this skill. +- **Generic by design:** to add a future version-pinned dataset, add a sibling + build script and a step block — the R2 layout, publish-version logic, and + upload gating are shared. + +### Sibling skills + +- `/update-module` — the currency gate's remediation (step 1). +- `/release-checklist` — check 15 probes this exact bundle and recommends this + skill when it 404s. diff --git a/.claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh b/.claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh new file mode 100755 index 000000000..e0dff5664 --- /dev/null +++ b/.claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh @@ -0,0 +1,129 @@ +#!/usr/bin/env bash +set -euo pipefail + +# Build the AMRFinder+ database tarball inside the amrfinderplus module's pinned +# container. This script owns the build recipe formerly carried by the (now +# removed) modules/amrfinderplus/update/ Nextflow module. +# +# It reads the pinned container image + tool version from the run module's +# config (modules/amrfinderplus/run/module.config) so a tool version bump flows +# through automatically, then runs `amrfinder_update` in that container and +# packages the result as amrfinderplus.tar.gz. + +usage() { + cat >&2 <<'EOF' +Usage: build-amrfinderplus-db.sh --bactopia-path [--runtime docker|singularity] [--outdir ] + + --bactopia-path Path to the Bactopia repository (required). + --runtime Container runtime: docker (default) or singularity. + --outdir Output directory for the tarball + (default: /logs/dataset-builds/). +EOF + exit 1 +} + +BACTOPIA_PATH="" +RUNTIME="docker" +OUTDIR="" + +while [[ $# -gt 0 ]]; do + case "$1" in + --bactopia-path) BACTOPIA_PATH="${2:-}"; shift 2 ;; + --runtime) RUNTIME="${2:-}"; shift 2 ;; + --outdir) OUTDIR="${2:-}"; shift 2 ;; + -h|--help) usage ;; + *) echo "ERROR: unknown argument: $1" >&2; usage ;; + esac +done + +[[ -n "$BACTOPIA_PATH" ]] || { echo "ERROR: --bactopia-path is required" >&2; usage; } +[[ -d "$BACTOPIA_PATH" ]] || { echo "ERROR: bactopia path not found: $BACTOPIA_PATH" >&2; exit 1; } + +case "$RUNTIME" in + docker|singularity) ;; + *) echo "ERROR: --runtime must be 'docker' or 'singularity'" >&2; exit 1 ;; +esac + +MODULE_CONFIG="$BACTOPIA_PATH/modules/amrfinderplus/run/module.config" +[[ -f "$MODULE_CONFIG" ]] || { echo "ERROR: module.config not found: $MODULE_CONFIG" >&2; exit 1; } + +# Pinned images live in the run module's config (ext.docker / ext.image). +DOCKER_IMAGE=$(grep -oP 'ext\.docker\s*=\s*"\K[^"]+' "$MODULE_CONFIG" | head -1) +SING_IMAGE=$(grep -oP 'ext\.image\s*=\s*"\K[^"]+' "$MODULE_CONFIG" | head -1) +[[ -n "$DOCKER_IMAGE" ]] || { echo "ERROR: could not parse ext.docker from $MODULE_CONFIG" >&2; exit 1; } +[[ -n "$SING_IMAGE" ]] || { echo "ERROR: could not parse ext.image from $MODULE_CONFIG" >&2; exit 1; } + +# ext.docker is a bare Docker Hub-style repo (e.g. biocontainers/...); Nextflow +# prepends params.registry (default quay.io) at run time, so we do the same. If +# the image's first path segment already looks like a host (contains '.' or ':'), +# it is left untouched. +REGISTRY=$(grep -oP 'registry\s*=\s*"\K[^"]+' "$BACTOPIA_PATH/conf/params.config" | head -1) +REGISTRY="${REGISTRY:-quay.io}" +first_segment="${DOCKER_IMAGE%%/*}" +if [[ "$DOCKER_IMAGE" == "$first_segment" || ( "$first_segment" != *.* && "$first_segment" != *:* ) ]]; then + FULL_IMAGE="$REGISTRY/$DOCKER_IMAGE" +else + FULL_IMAGE="$DOCKER_IMAGE" +fi + +if [[ -z "$OUTDIR" ]]; then + TS=$(date +%Y%m%d_%H%M%S) + OUTDIR="$BACTOPIA_PATH/logs/dataset-builds/$TS" +fi +mkdir -p "$OUTDIR" +OUTDIR=$(cd "$OUTDIR" && pwd) + +# Recipe executed inside the container; /work is bound to $OUTDIR. Command +# substitutions ($()) are evaluated by the container's shell at runtime. +read -r -d '' BODY <<'EOF' || true +set -euo pipefail +cd /work +rm -rf amrfinderplus-temp amrfinderplus +mkdir -p amrfinderplus-temp +amrfinder_update -d amrfinderplus-temp +mv "amrfinderplus-temp/$(readlink amrfinderplus-temp/latest)" amrfinderplus/ +tar czvf amrfinderplus.tar.gz amrfinderplus/ +amrfinder --version > TOOL_VERSION +echo $(amrfinder --database amrfinderplus --database_version 2> /dev/null) | rev | cut -f1 -d' ' | rev > DB_VERSION +rm -rf amrfinderplus-temp amrfinderplus +EOF + +echo ">> Building AMRFinder+ database" >&2 +echo ">> runtime=$RUNTIME image=$FULL_IMAGE outdir=$OUTDIR" >&2 + +if [[ "$RUNTIME" == "docker" ]]; then + command -v docker >/dev/null 2>&1 || { echo "ERROR: docker not found" >&2; exit 1; } + docker run --rm --user "$(id -u):$(id -g)" \ + -v "$OUTDIR":/work -w /work "$FULL_IMAGE" \ + bash -c "$BODY" +else + RUNNER="" + if command -v apptainer >/dev/null 2>&1; then + RUNNER="apptainer" + elif command -v singularity >/dev/null 2>&1; then + RUNNER="singularity" + else + echo "ERROR: singularity/apptainer not found" >&2 + exit 1 + fi + # Reuse the same registry-qualified image via docker:// so both runtimes match. + "$RUNNER" exec --bind "$OUTDIR":/work "docker://$FULL_IMAGE" bash -c "$BODY" +fi + +TARBALL="$OUTDIR/amrfinderplus.tar.gz" +[[ -s "$TARBALL" ]] || { echo "ERROR: build produced no tarball at $TARBALL" >&2; exit 1; } + +SHA=$(sha256sum "$TARBALL" | cut -d' ' -f1) +TOOL_VERSION=$(cat "$OUTDIR/TOOL_VERSION" 2>/dev/null || echo "unknown") +DB_VERSION=$(cat "$OUTDIR/DB_VERSION" 2>/dev/null || echo "unknown") + +cat <` to the command. + Parse the JSON from that file. If the user specified a module name, add `--module ` to the command **and do not write the record** (a filtered run is not a full-repo check — only an unfiltered scan is a valid `/release-checklist` freshness record). `logs/` is gitignored, so the record is scratch, not a tracked file. 2. Parse the JSON output. Separate entries into three categories: - **Needs update** (`needs_update: true`): ready for automatic update diff --git a/.gitignore b/.gitignore index 1f43a3057..d32d876ab 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ trace.txt* **/.nf-test/* **/.nf-test-*.nf logs/ +WATCHDOG.yml # Conda Build data/conda/channeldata.json @@ -28,6 +29,7 @@ data/conda/noarch/ # Claude .claude/plans/ .claude/handoffs/ +.claude/skills/*-workspace/ # temp v4 folders old-bactopia/ diff --git a/.vscode/settings.json b/.vscode/settings.json index e9adda44a..4ee806fb6 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -92,6 +92,7 @@ "Binations", "bioconda", "biocontainers", + "bioinformatic", "bioinformatics", "bionj", "bioperl", @@ -319,6 +320,7 @@ "genomesize", "genotyphi", "genotyping", + "genpept", "Gerken", "getenv", "getref", @@ -614,6 +616,7 @@ "nfconfig", "nfcore", "nfdir", + "nftest", "nftignore", "ngmaster", "NHBA", @@ -655,6 +658,7 @@ "openpyxl", "opid", "Oppong", + "orcid", "ords", "ortholog", "orthologous", @@ -921,6 +925,8 @@ "stutzeri", "Stutzerimonas", "subdir", + "subsampled", + "subsamples", "subsampling", "Subtyping", "Subworkflow", diff --git a/CHANGELOG.md b/CHANGELOG.md index f6f2f8fa6..7f34de9fa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ sidebar_position: 5000 - Bactopia Tools (`bactopia --wf `) - `staphscan` - Genome-based surveillance analysis of _Staphylococcus aureus_ - `traitar` - Predict phenotypic traits from microbial genomes +- New Skills + - `/update-datasets` to rebuild and publish version-pinned datasets - Added StaphSCAN to the Staphtyper and Merlin subworkflows - Deacon as the default host read scrubber (replaces nohuman as default) - Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules @@ -24,7 +26,21 @@ sidebar_position: 5000 - subworkflow emits `assemblies` from the named `fna` field, and `reference` from `gbff` when `--format genbank` is used (Snippy needs an annotated reference), otherwise `fna` - Bump internal bactopia-* pipeline tool versions - - `bactopia-gather`: 1.0.5 -> 1.0.6 + - `bactopia-gather`: 1.0.5 -> 1.2.0 +- bump program versions in modules + - `abritamr`: 1.2.0 -> 1.3.0 + - `busco`: 6.0.0 -> 6.1.0 + - `defense-finder`: 2.0.1 -> 3.0.0 + - `eggnog-mapper`: 2.1.13 -> 2.1.15 + - `gtdbtk`: 2.7.1 -> 2.7.2 + - `iqtree`: 3.1.1 -> 3.1.3 + - `mash`: 2.3--hb105d93_10 -> 2.3--hf85e966_11 + - `mlst`: 2.33.1 -> 2.35.0 + - `ngmaster`: 2.0.0 -> 2.1.0 + - `panaroo`: 1.6.0 -> 1.8.0 + - `phispy`: 5.0.6 -> 5.0.10 + - `rgi`: 6.0.5 -> 6.0.8 + - `staphscan`: 0.3.1 -> 0.4.1 ### `Changed` @@ -37,38 +53,27 @@ sidebar_position: 5000 assembly filename (`GCF_020736045.1_ASM2073604v1_genomic`), which changes output paths and tree/matrix labels - `snippy --accession` requires `--format genbank`, since Snippy needs an annotated reference +- `bactopia gather` now downloads assemblies with `genome-dl` instead of `ncbi-genome-download` + - `--no_cache` is no longer available (it only tuned `ncbi-genome-download`'s summary cache) - Deacon modules now use bactopia-teton container instead of standalone deacon container - Teton and scrubber workflows default to deacon instead of nohuman for host read removal - cleanyerreads workflow supports `--use_deacon` flag for host read removal -- Every generated workflow `nextflow.config` now declares `params.bactopia_dir`, an absolute - anchor to the Bactopia repo root, so `module.config` can reference vendored data under - `data/` regardless of tier or launch directory +- Added `params.bactopia_dir` which anchors to the Bactopia repo root so `data/` can be reference by all workflows +- Centralized the pipeline version and `nf-bactopia@` plugin pin for module/subworkflow tests into `conf/test_base.config`; each `tests/nextflow.config` now `includeConfig`s it instead of repeating the values, so a version bump touches one file ### `Fixed` - float parameters being interpreted as strings in CLI -- `--prokka_proteins` defaulting to `./data/proteins.faa`, which Nextflow resolves against the - launch directory rather than the repo. Only runs launched from the repo root picked up the - bundled protein set; every other run failed with - `Input file './data/proteins.faa' does not exist`. The default is now anchored on the new - `params.bactopia_dir` and resolves to `data/proteins.faa` from any working directory -- `fastani` documenting a `--fastani_skip_pairwise` parameter that does not exist. The parameter - the workflow actually reads is `--fastani_pairwise`, so neither `--help` nor the docs site - mentioned the only way to run FastANI without `--fastani_reference`, `--accession`, - `--accessions`, or `--species`. The requirement is now stated in the `fastani` GroovyDoc +- `--prokka_proteins` not being found in non-Bactopia workflows +- `--fastani_skip_pairwise` parameter that does not exist - `mlst` and `amrfinderplus` Bactopia Tools failing immediately with `ERROR ~ Path string cannot - be empty` when run without `--mlst_db` / `--amrfinderplus_db` ([#673](https://github.com/bactopia/bactopia/issues/673)). - Both params defaulted to `""`, and Nextflow's static typing coerces the default to a `Path` at - parameter declaration, before the workflow body runs, so `amrfinderplus`'s existing - `if (params.amrfinderplus_db)` fallback was unreachable. Both now default to `null` -- `mlst` Bactopia Tool having no way to source the PubMLST database automatically. It passed - `params.mlst_db` straight through, so `--mlst_db` was effectively required. It now falls back to - the `bactopia_datasets` subworkflow, matching `amrfinderplus` -- `mobsuite` failing on any sample with no reconstructed plasmids. After `chromosome.fasta` was - moved out of `supplemental/`, the cleanup step ran `gzip supplemental/*.fasta` on an unguarded - glob; with no plasmids nothing matched, `gzip` exited non-zero, and Nextflow's `bash -ue` - aborted the task even though `mob_recon` had succeeded. Cleanup now uses `find -exec`, which - is a no-op when there is nothing to compress + be empty` when run without `--mlst_db` / `--amrfinderplus_db` ([#673](https://github.com/bactopia/bactopia/issues/673)) +- `mlst` Bactopia Tool not falling back on bactopia/datasets +- `mobsuite` failing on any sample without plasmids due to compressing non-existent files +- removed unused `amrfinderplus/update` module +- `rgi` failing with `unrecognized arguments: --num_threads` after the 6.0.8 bump (renamed to `--threads`) +- `rgi_exclude_nudge` emitting the removed `--exclude_nudge` flag; replaced with `rgi_include_nudge` which passes RGI 6's opt-in `--include_nudge` +- `bactopia datasets` tests requesting a version-pinned `mlst.tar.gz` (404); `mlst_url` has been version-less since v4.0.0 ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/CITATION.cff b/CITATION.cff index f0c2c7b81..f2c147a12 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,4 +10,4 @@ authors: title: "Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020)" doi: 10.1128/mSystems.00190-20 url: "https://github.com/bactopia/bactopia" -version: 4.0.0 +version: 4.1.0 diff --git a/CLAUDE.md b/CLAUDE.md index 956faea20..4ec3faf89 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -93,6 +93,7 @@ When working with this codebase: 3. **For documenting modules**: Read [.claude/docs/standards/05-module-documentation.md](.claude/docs/standards/05-module-documentation.md) for complete methodology and examples 4. **For documenting subworkflows**: Read [.claude/docs/standards/04-subworkflow-documentation.md](.claude/docs/standards/04-subworkflow-documentation.md) for complete methodology and examples 5. **Always check** [.claude/docs/standards/03-technical-specs.md](.claude/docs/standards/03-technical-specs.md) for variable naming and technical conventions +6. **Always use the `bactopia-dev` conda env for all project tooling** — `ruff`, `bactopia-*` CLIs (`bactopia-lint`, `bactopia-test`, `bactopia-merge-schemas`, `bactopia-catalog`, `bactopia-citations`), and `nf-test`. Invoke via `conda run -n bactopia-dev ` (or activate the env first). Never report a check as SKIP because a tool is "not on PATH" without trying this env. ## Quick Reference diff --git a/bin/bactopia b/bin/bactopia index f6d4bab37..7b7a7010c 100755 --- a/bin/bactopia +++ b/bin/bactopia @@ -1,5 +1,5 @@ #!/usr/bin/env bash -VERSION=4.0.1 +VERSION=4.1.0 CONDA_ENV=$(which bactopia | sed 's=bin/bactopia==') BACTOPIA_NF="${CONDA_ENV}/share/bactopia-${VERSION}" diff --git a/catalog.json b/catalog.json index d4d29634c..5a5e8619d 100644 --- a/catalog.json +++ b/catalog.json @@ -1,7 +1,7 @@ { "version": "1.0", - "generated": "2026-07-27T21:57:49Z", - "bactopia_version": "4.0.1", + "generated": "2026-07-28T22:44:08Z", + "bactopia_version": "4.1.0", "bactopia_py_version": "2.2.0", "nf_bactopia_version": "2.1.6", "modules": { @@ -60,7 +60,7 @@ "process_name": "abritamr", "tool": { "name": "abritamr", - "version": "1.2.0" + "version": "1.3.0" }, "takes": [ "fna" @@ -141,31 +141,6 @@ ] } }, - "amrfinderplus_update": { - "description": "Download and index the latest AMRFinder+ database.", - "path": "modules/amrfinderplus/update/", - "scope": "sample", - "process_name": "amrfinderplus_update", - "tool": { - "name": "ncbi-amrfinderplus", - "version": "4.2.7" - }, - "emits": [ - "db" - ], - "tags": { - "complexity": "simple", - "input_type": "none", - "output_type": "single", - "features": [ - "internet-access", - "archive-output", - "compression", - "database-dependent", - "no-test" - ] - } - }, "ariba_getref": { "description": "Download and prepare reference databases for ARIBA analysis.", "path": "modules/ariba/getref/", @@ -299,7 +274,7 @@ "process_name": "gather", "tool": { "name": "bactopia-gather", - "version": "1.1.1" + "version": "1.2.0" }, "takes": [ "r1_files", @@ -708,7 +683,7 @@ "process_name": "busco", "tool": { "name": "busco", - "version": "6.0.0" + "version": "6.1.0" }, "takes": [ "fna" @@ -1001,7 +976,7 @@ "process_name": "defensefinder", "tool": { "name": "defense-finder", - "version": "2.0.1" + "version": "3.0.0" }, "takes": [ "faa" @@ -1036,7 +1011,7 @@ "process_name": "defensefinder", "tool": { "name": "defense-finder", - "version": "2.0.1" + "version": "3.0.0" }, "emits": [ "db" @@ -1085,7 +1060,7 @@ "process_name": "eggnog", "tool": { "name": "eggnog-mapper", - "version": "2.1.13" + "version": "2.1.15" }, "emits": [ "db", @@ -1109,7 +1084,7 @@ "process_name": "eggnog", "tool": { "name": "eggnog-mapper", - "version": "2.1.13" + "version": "2.1.15" }, "takes": [ "faa" @@ -1334,7 +1309,7 @@ "process_name": "gtdb", "tool": { "name": "gtdbtk", - "version": "2.7.1" + "version": "2.7.2" }, "takes": [ "fna" @@ -1364,7 +1339,7 @@ "process_name": "gtdbtk", "tool": { "name": "gtdbtk", - "version": "2.7.1" + "version": "2.7.2" }, "emits": [ "db", @@ -1469,7 +1444,7 @@ "process_name": "iqtree", "tool": { "name": "iqtree", - "version": "3.1.1" + "version": "3.1.3" }, "takes": [ "aln" @@ -1865,7 +1840,7 @@ "process_name": "mlst", "tool": { "name": "mlst", - "version": "2.33.1" + "version": "2.35.0" }, "takes": [ "fna" @@ -1956,7 +1931,7 @@ "process_name": "ngmaster", "tool": { "name": "ngmaster", - "version": "2.0.0" + "version": "2.1.0" }, "takes": [ "fna" @@ -2052,7 +2027,7 @@ "process_name": "panaroo_run", "tool": { "name": "panaroo", - "version": "1.6.0" + "version": "1.8.0" }, "takes": [ "gff" @@ -2136,7 +2111,7 @@ "process_name": "phispy", "tool": { "name": "phispy", - "version": "5.0.6" + "version": "5.0.10" }, "takes": [ "gbff" @@ -2309,7 +2284,7 @@ "process_name": "rgi_heatmap", "tool": { "name": "rgi", - "version": "6.0.5" + "version": "6.0.8" }, "takes": [ "json" @@ -2336,7 +2311,7 @@ "process_name": "rgi_main", "tool": { "name": "rgi", - "version": "6.0.5" + "version": "6.0.8" }, "takes": [ "fna" @@ -2869,7 +2844,7 @@ "process_name": "staphscan", "tool": { "name": "staphscan", - "version": "0.3.1" + "version": "0.4.1" }, "takes": [ "fna" diff --git a/conf/test_base.config b/conf/test_base.config new file mode 100644 index 000000000..a140c4e31 --- /dev/null +++ b/conf/test_base.config @@ -0,0 +1,26 @@ +// Params +params { + bactopia_version = '4.1.0' + bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" + condadir = "${params.bactopia_cache}/conda" + merge_folder = "merged-results" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + is_ci = true + + // Max Job Request Parameters + max_retry = 1 + max_time = 2.h + max_memory = 8.GB + max_cpus = 2 + + // Nextflow Profile Parameters + registry = "quay.io" + singularity_cache = "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = false + container_opts = "" +} + +// Plugin +plugins { + id 'nf-bactopia@2.1.6' +} diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 532e96dc4..350d9944d 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '4.0.1' %} +{% set version = '4.1.0' %} package: name: bactopia diff --git a/llms.txt b/llms.txt index be1811c88..31d478f32 100644 --- a/llms.txt +++ b/llms.txt @@ -34,7 +34,7 @@ All components use standardized GroovyDoc documentation and static typing. ## Modules (Tier 3) -105 tool-specific modules live under `modules/`. Each module directory contains: +104 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header - `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions - `tests/`: nf-test test cases diff --git a/modules/abricate/run/tests/main.nf.test.snap b/modules/abricate/run/tests/main.nf.test.snap index fec637ac8..0150626c5 100644 --- a/modules/abricate/run/tests/main.nf.test.snap +++ b/modules/abricate/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,7baef5ee36e4b70a7227723d89bf97ea" ] ], - "timestamp": "2026-04-29T11:15:41.488349212", + "timestamp": "2026-07-28T17:03:52.674364547", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abricate/run/tests/nextflow.config b/modules/abricate/run/tests/nextflow.config index 7d79268c9..22a37b5f2 100644 --- a/modules/abricate/run/tests/nextflow.config +++ b/modules/abricate/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ABRICATE_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/abricate/summary/tests/main.nf.test.snap b/modules/abricate/summary/tests/main.nf.test.snap index cc22b5005..0aca2db50 100644 --- a/modules/abricate/summary/tests/main.nf.test.snap +++ b/modules/abricate/summary/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,87422ca0c784de85ba93ac7352052d82" ] ], - "timestamp": "2026-04-29T11:15:37.997794062", + "timestamp": "2026-07-28T17:03:57.316909203", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abricate/summary/tests/nextflow.config b/modules/abricate/summary/tests/nextflow.config index 92b2a9601..0d58999da 100644 --- a/modules/abricate/summary/tests/nextflow.config +++ b/modules/abricate/summary/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ABRICATE_SUMMARY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../../run/module.config" diff --git a/modules/abritamr/run/module.config b/modules/abritamr/run/module.config index 11b173460..12bd61bcc 100644 --- a/modules/abritamr/run/module.config +++ b/modules/abritamr/run/module.config @@ -19,9 +19,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::abritamr=1.2.0".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/abritamr:1.2.0--pyh5707d69_1" - ext.image = "https://depot.galaxyproject.org/singularity/abritamr:1.2.0--pyh5707d69_1" + ext.toolName = "bioconda::abritamr=1.3.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/abritamr:1.3.0--pyh5707d69_0" + ext.image = "https://depot.galaxyproject.org/singularity/abritamr:1.3.0--pyh5707d69_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/abritamr/run/tests/main.nf.test.snap b/modules/abritamr/run/tests/main.nf.test.snap index 8b64ff003..7dcc951fe 100644 --- a/modules/abritamr/run/tests/main.nf.test.snap +++ b/modules/abritamr/run/tests/main.nf.test.snap @@ -15,10 +15,10 @@ "GCF_001682305.summary_virulence.tsv:md5,439b76b76818cbe8ec06bc82bd2711fe", "GCF_001682305.amrfinder.out:md5,5653ba9662232edc023dcc9606440e91", [ - "versions.yml:md5,ebc49c238ebaaaa54c98e7276f3f2aff" + "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-04-29T11:20:00.097478921", + "timestamp": "2026-07-28T17:08:01.106751519", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -40,10 +40,10 @@ "GCF_001682305.summary_virulence.tsv:md5,439b76b76818cbe8ec06bc82bd2711fe", "GCF_001682305.amrfinder.out:md5,5653ba9662232edc023dcc9606440e91", [ - "versions.yml:md5,ebc49c238ebaaaa54c98e7276f3f2aff" + "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-04-29T11:24:26.482969396", + "timestamp": "2026-07-28T17:12:26.782352417", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abritamr/run/tests/nextflow.config b/modules/abritamr/run/tests/nextflow.config index e82b1674b..2c5efde44 100644 --- a/modules/abritamr/run/tests/nextflow.config +++ b/modules/abritamr/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ABRITAMR_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/agrvate/tests/main.nf.test.snap b/modules/agrvate/tests/main.nf.test.snap index 1e800dd7c..3b477c2a5 100644 --- a/modules/agrvate/tests/main.nf.test.snap +++ b/modules/agrvate/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-04-29T11:15:55.590124401", + "timestamp": "2026-07-28T17:04:04.297911813", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-04-29T11:15:39.027066867", + "timestamp": "2026-07-28T17:03:50.7369451", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/agrvate/tests/nextflow.config b/modules/agrvate/tests/nextflow.config index 764a49f18..f2ff956b2 100644 --- a/modules/agrvate/tests/nextflow.config +++ b/modules/agrvate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of AGRVATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/amrfinderplus/run/tests/main.nf.test.snap b/modules/amrfinderplus/run/tests/main.nf.test.snap index 6046e4ff4..6acd0f633 100644 --- a/modules/amrfinderplus/run/tests/main.nf.test.snap +++ b/modules/amrfinderplus/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-04-29T11:15:49.829865356", + "timestamp": "2026-07-28T17:03:55.849652335", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-04-29T11:16:12.919706335", + "timestamp": "2026-07-28T17:04:18.867455838", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/amrfinderplus/run/tests/nextflow.config b/modules/amrfinderplus/run/tests/nextflow.config index e92a2356b..52bae2527 100644 --- a/modules/amrfinderplus/run/tests/nextflow.config +++ b/modules/amrfinderplus/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of AMRFINDERPLUS_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/amrfinderplus/update/main.nf b/modules/amrfinderplus/update/main.nf deleted file mode 100644 index 583729251..000000000 --- a/modules/amrfinderplus/update/main.nf +++ /dev/null @@ -1,59 +0,0 @@ -/** - * Download and index the latest AMRFinder+ database. - * - * Fetches the most recent [AMRFinder+](https://github.com/ncbi/amr) databases from NCBI, - * indexes them, and packages them into a tarball. - * - * @status stable - * @keywords bacteria, database, antimicrobial resistance, update, download, ncbi - * @tags complexity:simple input-type:none output-type:single features:internet-access,archive-output,compression,database-dependent,no-test - * @citation amrfinderplus - * - * @note Internal Maintenance - * This process is primarily used internally by Bactopia to build and update the - * built-in datasets. - * - * @output record(db, logs) - * - `db`: A compressed tarball of the latest AMRFinder+ database - */ -nextflow.enable.types = true - -// bactopia-lint: ignore M012,M017,M018,M022,M023,M024,M025,M026,M028 -process AMRFINDERPLUS_UPDATE { - tag "amrfinderplus-update" - label 'process_low' - - conda "${task.ext.condaDir}/${task.ext.toolName}" - container "${task.ext.container}" - - output: - record( - db: file("updater/amrfinderplus.tar.gz"), - logs: files("updater/logs/*", optional: true) - ) - - script: - """ - mkdir -p updater/logs - mkdir amrfinderplus-temp - amrfinder_update -d amrfinderplus-temp - mv amrfinderplus-temp/\$(readlink amrfinderplus-temp/latest) amrfinderplus/ - tar czvf amrfinderplus.tar.gz amrfinderplus/ - mv amrfinderplus.tar.gz updater/ - - # Move outputs to tool specific folder - cp .command.begin updater/logs/nf.command.begin - cp .command.err updater/logs/nf.command.err - cp .command.log updater/logs/nf.command.log - cp .command.out updater/logs/nf.command.out - cp .command.run updater/logs/nf.command.run - cp .command.sh updater/logs/nf.command.sh - cp .command.trace updater/logs/nf.command.trace - - cat <<-END_VERSIONS > updater/logs/versions.yml - "${task.process}": - amrfinderplus: \$(amrfinder --version) - amrfinderplus-database: \$(echo \$(echo \$(amrfinder --database amrfinderplus --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)) - END_VERSIONS - """ -} diff --git a/modules/amrfinderplus/update/module.config b/modules/amrfinderplus/update/module.config deleted file mode 100644 index bc2bea267..000000000 --- a/modules/amrfinderplus/update/module.config +++ /dev/null @@ -1,23 +0,0 @@ -params { - // No parameters -} - -process { - withName: 'AMRFINDERPLUS_UPDATE' { - ext.wf = params.wf - ext.scope = "sample" - ext.subdir = "" - ext.logs_subdir = "" - ext.process_name = "amrfinderplus_update" - storeDir = params.datasets_cache - - // Tool arguments - ext.args = "" - - // Environment information - ext.toolName = "bioconda::ncbi-amrfinderplus=4.2.7".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/ncbi-amrfinderplus:4.2.7--hf69ffd2_0" - ext.image = "https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:4.2.7--hf69ffd2_0" - ext.condaDir = "${params.condadir}" - } -} diff --git a/modules/amrfinderplus/update/schema.json b/modules/amrfinderplus/update/schema.json deleted file mode 100644 index 47572fbbb..000000000 --- a/modules/amrfinderplus/update/schema.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/amrfinderplus/update/schema.json", - "title": "AMRFinderPlus Update Module", - "description": "Download the latest AMRFinderPlus database", - "type": "object", - "$defs": { - "amrfinderplus_update_parameters": { - "title": "AMRFinderPlus Update Parameters", - "type": "object", - "description": "", - "default": "", - "fa_icon": "fas fa-exclamation-circle", - "properties": {} - } - }, - "allOf": [ - { - "$ref": "#/$defs/amrfinderplus_update_parameters" - } - ] -} diff --git a/modules/ariba/run/tests/main.nf.test.snap b/modules/ariba/run/tests/main.nf.test.snap index 173c0dab2..5d0e187bd 100644 --- a/modules/ariba/run/tests/main.nf.test.snap +++ b/modules/ariba/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2d20a87ab1578332cae79c947a52e8f8" ] ], - "timestamp": "2026-04-29T11:16:11.163361868", + "timestamp": "2026-07-28T17:04:24.901542508", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ariba/run/tests/nextflow.config b/modules/ariba/run/tests/nextflow.config index de63ff3ca..5472409c1 100644 --- a/modules/ariba/run/tests/nextflow.config +++ b/modules/ariba/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ARIBA_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/bactopia/assembler/tests/main.nf.test.snap b/modules/bactopia/assembler/tests/main.nf.test.snap index ec0c17fea..6036df2a9 100644 --- a/modules/bactopia/assembler/tests/main.nf.test.snap +++ b/modules/bactopia/assembler/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:30:20.139919124", + "timestamp": "2026-07-28T17:18:27.769304249", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -41,7 +41,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:34:21.859433895", + "timestamp": "2026-07-28T17:22:45.415299986", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -65,7 +65,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:33:59.04450709", + "timestamp": "2026-07-28T17:22:19.479954032", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -89,7 +89,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:32:34.46974438", + "timestamp": "2026-07-28T17:20:52.018603646", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -113,7 +113,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:33:02.375790423", + "timestamp": "2026-07-28T17:21:20.503729652", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -137,7 +137,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:18:07.066187784", + "timestamp": "2026-07-28T17:06:14.440697896", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -161,7 +161,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:18:51.640725893", + "timestamp": "2026-07-28T17:06:56.934841934", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -185,7 +185,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-04-29T11:23:08.642297911", + "timestamp": "2026-07-28T17:11:00.59649405", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/assembler/tests/nextflow.config b/modules/bactopia/assembler/tests/nextflow.config index 173d68ca6..5e8ded2fc 100644 --- a/modules/bactopia/assembler/tests/nextflow.config +++ b/modules/bactopia/assembler/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ASSEMBLER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,26 +11,11 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 12 - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - // Module-specific defaults skip_compression = false keep_all_files = false diff --git a/modules/bactopia/datasets/tests/nextflow.config b/modules/bactopia/datasets/tests/nextflow.config index 786efd126..3bce1f353 100644 --- a/modules/bactopia/datasets/tests/nextflow.config +++ b/modules/bactopia/datasets/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of DATASETS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,30 +11,12 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults datasets_cache = "${params.bactopia_cache}/datasets" amrfinderplus_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/amrfinderplus.tar.gz" - mlst_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/mlst.tar.gz" + mlst_url = "https://datasets.bactopia.com/datasets/mlst.tar.gz" mash_url = "https://datasets.bactopia.com/datasets/mash-refseq88.k21.msh.xz" sourmash_url = "https://datasets.bactopia.com/datasets/gtdb-rs207.genomic-reps.dna.k31.lca.json.gz" } diff --git a/modules/bactopia/gather/main.nf b/modules/bactopia/gather/main.nf index 278849c5d..b6300b3d4 100644 --- a/modules/bactopia/gather/main.nf +++ b/modules/bactopia/gather/main.nf @@ -81,7 +81,7 @@ process GATHER { ], logs: files("*.{log,err}", optional: true), nf_logs: files(".command.*"), - versions: files("versions.yml", optional: true) + versions: files("versions.yml") ) script: @@ -115,9 +115,7 @@ process GATHER { ) // WF specific parameters - def String no_cache = task.ext.no_cache ? '-N' : '' def String archive = task.ext.use_ena ? (task.attempt >= 4 ? "SRA" : "ENA") : "SRA" - def String section = runtype == 'assembly_accession' ? (prefix.startsWith('GCF') ? 'refseq' : 'genbank') : '' def Integer fcov = task.ext.coverage.toInteger() == 0 ? 150 : Math.round(task.ext.coverage.toInteger() * 1.5) // Determine what reads we have based on the explicit slots @@ -260,14 +258,12 @@ process GATHER { rm check-assembly-accession.txt fi - # Download from NCBI assembly and simulate reads - ncbi-genome-download bacteria -o ./ -F fasta -p ${task.cpus} \\ - -u "https://ftp.ncbi.nlm.nih.gov/genomes" \\ - -s ${section} -A accession.txt -r 50 ${no_cache} + # Download from NCBI Datasets and simulate reads + genome-dl --formats fasta --outdir ./ --cpus ${task.cpus} --max-attempts ${task.ext.max_retry} \\ + --prefix ${prefix} --accession ${prefix} - # Nested directories are not easy to predict, but there should only be a - # single assembly file. The assembly version (e.g., GCF_000005845.2 --> .2) - # is removed for consistency. + # genome-dl names the assembly by its resolved accession. The assembly version + # (e.g., GCF_000005845.2 --> .2) is removed for consistency. find . -name "*${prefix}*.fna.gz" | xargs -I {} mv {} assembly/ rename 's/(GC[AF]_\\d+).*/\$1.fna.gz/' assembly/* gzip -cd assembly/${prefix}.fna.gz > ${prefix}-art.fna @@ -357,7 +353,7 @@ process GATHER { art: \$(echo \$(art_illumina --help 2>&1) | sed 's/^.*Version //;s/ .*\$//') fastq-dl: \$(echo \$(fastq-dl --version 2>&1) | sed 's/fastq-dl, version //') fastq-scan: \$(echo \$(fastq-scan -v 2>&1) | sed 's/fastq-scan //') - ncbi-genome-download: \$(echo \$(ncbi-genome-download --version 2>&1)) + genomedl: \$(echo \$(genome-dl --version 2>&1) | sed 's/.*version //') pigz: \$(echo \$(pigz --version 2>&1) | sed 's/pigz //') END_VERSIONS """ diff --git a/modules/bactopia/gather/module.config b/modules/bactopia/gather/module.config index 5b00cccb3..4400e555d 100644 --- a/modules/bactopia/gather/module.config +++ b/modules/bactopia/gather/module.config @@ -7,7 +7,6 @@ params { min_genome_size = 100000 min_proportion = 0.5 min_reads = 7472 - no_cache = false skip_fastq_check = false use_ena = false } @@ -24,9 +23,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::bactopia-gather=1.1.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/bactopia-gather:1.1.1--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/bactopia-gather:1.1.1--hdfd78af_0" + ext.toolName = "bioconda::bactopia-gather=1.2.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/bactopia-gather:1.2.0--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/bactopia-gather:1.2.0--hdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters @@ -35,7 +34,6 @@ process { ext.min_basepairs = params.min_basepairs ext.min_proportion = params.min_proportion ext.min_reads = params.min_reads - ext.no_cache = params.no_cache ext.sampleseed = params.sampleseed ext.skip_compression = params.skip_compression ext.skip_fastq_check = params.skip_fastq_check diff --git a/modules/bactopia/gather/schema-cleanyerreads.json b/modules/bactopia/gather/schema-cleanyerreads.json index 68e7cbd9b..15e01ed5f 100644 --- a/modules/bactopia/gather/schema-cleanyerreads.json +++ b/modules/bactopia/gather/schema-cleanyerreads.json @@ -88,12 +88,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-globe-europe", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-save", - "hidden": true } } } diff --git a/modules/bactopia/gather/schema-teton.json b/modules/bactopia/gather/schema-teton.json index 27b747332..a2122dc43 100644 --- a/modules/bactopia/gather/schema-teton.json +++ b/modules/bactopia/gather/schema-teton.json @@ -88,12 +88,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-globe-europe", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-save", - "hidden": true } } } diff --git a/modules/bactopia/gather/schema.json b/modules/bactopia/gather/schema.json index 5f2eaed51..dffaf2836 100644 --- a/modules/bactopia/gather/schema.json +++ b/modules/bactopia/gather/schema.json @@ -74,12 +74,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-toggle-on", - "hidden": true } } } diff --git a/modules/bactopia/gather/tests/main.nf.test.snap b/modules/bactopia/gather/tests/main.nf.test.snap index b103bf00e..83c91d7e9 100644 --- a/modules/bactopia/gather/tests/main.nf.test.snap +++ b/modules/bactopia/gather/tests/main.nf.test.snap @@ -16,10 +16,10 @@ }, "output-meta.tsv:md5,ef455a74203f7b19de75cb17a98cb547", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:16:29.989103896", + "timestamp": "2026-07-28T17:04:53.278324761", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -42,10 +42,10 @@ }, "output-meta.tsv:md5,ba9712352bf788edfdfbf6d059dbc042", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:16:52.590715521", + "timestamp": "2026-07-28T17:05:18.23295091", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -67,10 +67,10 @@ "species": "Portiera aleyrodidarum" }, [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:18:31.051121254", + "timestamp": "2026-07-28T17:07:02.236536952", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -92,10 +92,10 @@ "species": "Portiera aleyrodidarum" }, [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:18:11.586314321", + "timestamp": "2026-07-28T17:06:40.90510727", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -118,10 +118,10 @@ }, "SRR2838702-meta.tsv:md5,1a1053e05f4f7a7407b6a1c03c74cd75", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:17:29.942675107", + "timestamp": "2026-07-28T17:05:54.566859301", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -144,10 +144,10 @@ }, "output-meta.tsv:md5,83fb00c77440761635fd0606ebddbec0", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:17:51.45634273", + "timestamp": "2026-07-28T17:06:16.525974229", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -170,10 +170,10 @@ }, "output-meta.tsv:md5,64f8cba4de7e40198f70b08bfb166a13", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:15:49.823379114", + "timestamp": "2026-07-28T17:04:06.350260305", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -196,10 +196,10 @@ }, "output-meta.tsv:md5,d350d0a30825ec8a049363594e5ff9dd", [ - "versions.yml:md5,837f65a9cb0c03f876b433e027c58725" + "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-04-29T11:16:08.925459823", + "timestamp": "2026-07-28T17:04:29.711658336", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/gather/tests/nextflow.config b/modules/bactopia/gather/tests/nextflow.config index b6633d628..37f406206 100644 --- a/modules/bactopia/gather/tests/nextflow.config +++ b/modules/bactopia/gather/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GATHER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults coverage = 100 diff --git a/modules/bactopia/qc/tests/main.nf.test.snap b/modules/bactopia/qc/tests/main.nf.test.snap index c596b2ec9..6134b07e1 100644 --- a/modules/bactopia/qc/tests/main.nf.test.snap +++ b/modules/bactopia/qc/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-04-29T11:17:05.661396493", + "timestamp": "2026-07-28T17:05:14.605830198", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -41,7 +41,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-04-29T11:18:09.002888188", + "timestamp": "2026-07-28T17:06:17.640161203", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -65,7 +65,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-04-29T11:20:54.528982484", + "timestamp": "2026-07-28T17:08:57.462133171", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -89,7 +89,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-04-29T11:19:01.400915676", + "timestamp": "2026-07-28T17:07:08.017750891", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -113,7 +113,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-04-29T11:21:35.403721612", + "timestamp": "2026-07-28T17:09:37.663643786", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/qc/tests/nextflow.config b/modules/bactopia/qc/tests/nextflow.config index 2c23ea722..9a6acf142 100644 --- a/modules/bactopia/qc/tests/nextflow.config +++ b/modules/bactopia/qc/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of QC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults coverage = 0 diff --git a/modules/bactopia/sketcher/tests/main.nf.test.snap b/modules/bactopia/sketcher/tests/main.nf.test.snap index d68cb450e..1c48bb473 100644 --- a/modules/bactopia/sketcher/tests/main.nf.test.snap +++ b/modules/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,559fcd38f7410952b8da3f25f165d6fd" ] ], - "timestamp": "2026-04-29T11:18:09.554728941", + "timestamp": "2026-07-28T17:06:23.390221639", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/sketcher/tests/nextflow.config b/modules/bactopia/sketcher/tests/nextflow.config index c48a53a5b..5171b2b83 100644 --- a/modules/bactopia/sketcher/tests/nextflow.config +++ b/modules/bactopia/sketcher/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SKETCHER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/bactopia/teton/tests/main.nf.test.snap b/modules/bactopia/teton/tests/main.nf.test.snap index 25cfda13d..2d0808857 100644 --- a/modules/bactopia/teton/tests/main.nf.test.snap +++ b/modules/bactopia/teton/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-04-29T11:15:38.449618682", + "timestamp": "2026-07-28T17:03:50.235609268", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-04-29T11:15:55.492042681", + "timestamp": "2026-07-28T17:04:03.989943423", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/teton/tests/nextflow.config b/modules/bactopia/teton/tests/nextflow.config index f16cf2b16..5612d6675 100644 --- a/modules/bactopia/teton/tests/nextflow.config +++ b/modules/bactopia/teton/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BACTOPIA_SAMPLESHEET (teton) nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,26 +11,8 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true outdir = "bactopia" - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/bakta/run/tests/main.nf.test.snap b/modules/bakta/run/tests/main.nf.test.snap index 0264701c6..7b9f85653 100644 --- a/modules/bakta/run/tests/main.nf.test.snap +++ b/modules/bakta/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-04-29T11:20:00.580493161", + "timestamp": "2026-07-28T17:08:03.063640921", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-04-29T11:22:53.418790016", + "timestamp": "2026-07-28T17:11:00.780109231", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bakta/run/tests/nextflow.config b/modules/bakta/run/tests/nextflow.config index 49117b422..2761c6aec 100644 --- a/modules/bakta/run/tests/nextflow.config +++ b/modules/bakta/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BAKTA_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/blast/blastn/tests/main.nf.test.snap b/modules/blast/blastn/tests/main.nf.test.snap index 636fa0781..67cb717f4 100644 --- a/modules/blast/blastn/tests/main.nf.test.snap +++ b/modules/blast/blastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,45d0dac48620078713131f03b02bd14a" ] ], - "timestamp": "2026-04-29T11:15:30.048855529", + "timestamp": "2026-07-28T17:03:46.984825239", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastn/tests/nextflow.config b/modules/blast/blastn/tests/nextflow.config index df31131be..34fd95e54 100644 --- a/modules/blast/blastn/tests/nextflow.config +++ b/modules/blast/blastn/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BLAST_BLASTN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/blast/blastp/tests/main.nf.test.snap b/modules/blast/blastp/tests/main.nf.test.snap index be8ce4f70..36f0e78a9 100644 --- a/modules/blast/blastp/tests/main.nf.test.snap +++ b/modules/blast/blastp/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,617451a4191edeef7d2c7fb101c1ac14" ] ], - "timestamp": "2026-04-29T11:15:31.839259609", + "timestamp": "2026-07-28T17:03:47.934334506", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastp/tests/nextflow.config b/modules/blast/blastp/tests/nextflow.config index b0f7240ae..f8fcaba8c 100644 --- a/modules/blast/blastp/tests/nextflow.config +++ b/modules/blast/blastp/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BLAST_BLASTP nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/blast/blastx/tests/main.nf.test.snap b/modules/blast/blastx/tests/main.nf.test.snap index f08d01695..93d635b4b 100644 --- a/modules/blast/blastx/tests/main.nf.test.snap +++ b/modules/blast/blastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6a3a4c2a4204ac747af921720f265d86" ] ], - "timestamp": "2026-04-29T11:15:31.209848107", + "timestamp": "2026-07-28T17:03:53.49461217", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastx/tests/nextflow.config b/modules/blast/blastx/tests/nextflow.config index 5387cc21e..6f93ba7ae 100644 --- a/modules/blast/blastx/tests/nextflow.config +++ b/modules/blast/blastx/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BLAST_BLASTX nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/blast/tblastn/tests/main.nf.test.snap b/modules/blast/tblastn/tests/main.nf.test.snap index cb49486d9..54132b077 100644 --- a/modules/blast/tblastn/tests/main.nf.test.snap +++ b/modules/blast/tblastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,24c7db9cd7b317dcf8ad2057a04b2860" ] ], - "timestamp": "2026-04-29T11:15:30.007079346", + "timestamp": "2026-07-28T17:03:56.595666724", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastn/tests/nextflow.config b/modules/blast/tblastn/tests/nextflow.config index aa0e88ae6..51c06d035 100644 --- a/modules/blast/tblastn/tests/nextflow.config +++ b/modules/blast/tblastn/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BLAST_TBLASTN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/blast/tblastx/tests/main.nf.test.snap b/modules/blast/tblastx/tests/main.nf.test.snap index 5e474f736..d83923efb 100644 --- a/modules/blast/tblastx/tests/main.nf.test.snap +++ b/modules/blast/tblastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2d402efb20baa10e7b3af88ef3f2312d" ] ], - "timestamp": "2026-04-29T11:15:28.369354558", + "timestamp": "2026-07-28T17:03:48.342241056", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastx/tests/nextflow.config b/modules/blast/tblastx/tests/nextflow.config index 5bbb21775..3050633e2 100644 --- a/modules/blast/tblastx/tests/nextflow.config +++ b/modules/blast/tblastx/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BLAST_TBLASTX nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/bracken/tests/main.nf.test.snap b/modules/bracken/tests/main.nf.test.snap index 2d3590549..db75e2f15 100644 --- a/modules/bracken/tests/main.nf.test.snap +++ b/modules/bracken/tests/main.nf.test.snap @@ -16,10 +16,10 @@ "SRR2838702.bracken.report.txt:md5,3ca9ddfeb074bce0b9fd1e8b8b9c8443", "SRR2838702.bracken.abundances.txt:md5,bfc7aea2ef689c21fdab164d29d2d57b", [ - "versions.yml:md5,1c58acfb3b27362db6c664d6757c6d53" + "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" ] ], - "timestamp": "2026-04-29T11:16:08.392324412", + "timestamp": "2026-07-28T17:04:36.177909247", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -38,14 +38,14 @@ "teton_reads": "SRR2838702SE.fastq.gz" }, "SRR2838702.bracken.tsv:md5,327dffe42a06c5819893b9043fc62f1a", - "SRR2838702.kraken2.report.txt:md5,8f8118f0d4eb6cef15f76c5c1fe880b8", - "SRR2838702.bracken.report.txt:md5,03fceefeff81b30a0fd7390584b5e5aa", + "SRR2838702.kraken2.report.txt:md5,d883be153ee044e74a9504c128f20ccd", + "SRR2838702.bracken.report.txt:md5,2ed70b1d772694c9737e5c817efd2d97", "SRR2838702.bracken.abundances.txt:md5,64fb9c79e36082acae54ead9cc8dcf83", [ - "versions.yml:md5,1c58acfb3b27362db6c664d6757c6d53" + "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" ] ], - "timestamp": "2026-04-29T11:19:50.777475925", + "timestamp": "2026-07-28T17:10:34.742056394", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bracken/tests/nextflow.config b/modules/bracken/tests/nextflow.config index 50eeb8438..d170f5674 100644 --- a/modules/bracken/tests/nextflow.config +++ b/modules/bracken/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BRACKEN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,10 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 12 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/btyper3/tests/main.nf.test.snap b/modules/btyper3/tests/main.nf.test.snap index c96f5b027..4a8f328dd 100644 --- a/modules/btyper3/tests/main.nf.test.snap +++ b/modules/btyper3/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-04-29T11:19:23.171937712", + "timestamp": "2026-07-28T17:07:30.205684975", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-04-29T11:17:24.997856437", + "timestamp": "2026-07-28T17:05:35.854705389", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/btyper3/tests/nextflow.config b/modules/btyper3/tests/nextflow.config index 55f16cc0f..2fe481d3f 100644 --- a/modules/btyper3/tests/nextflow.config +++ b/modules/btyper3/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BTYPER3 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/busco/module.config b/modules/busco/module.config index c0cdd6daf..037b7c51e 100644 --- a/modules/busco/module.config +++ b/modules/busco/module.config @@ -34,9 +34,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::busco=6.0.0".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/busco:6.0.0--pyhdfd78af_3" - ext.image = "https://depot.galaxyproject.org/singularity/busco:6.0.0--pyhdfd78af_3" + ext.toolName = "bioconda::busco=6.1.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/busco:6.1.0--pyhdfd78af_1" + ext.image = "https://depot.galaxyproject.org/singularity/busco:6.1.0--pyhdfd78af_1" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/busco/tests/main.nf.test.snap b/modules/busco/tests/main.nf.test.snap index 2f758591d..a3552790c 100644 --- a/modules/busco/tests/main.nf.test.snap +++ b/modules/busco/tests/main.nf.test.snap @@ -11,10 +11,10 @@ }, "SRR2838702-summary.txt:md5,d1cbbfb9ab7dee0204bfa26f3b982620", [ - "versions.yml:md5,f0c1c6e03db9f8846867b50f08126e1b" + "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-04-29T11:16:54.42682481", + "timestamp": "2026-07-28T19:41:02.471307985", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -32,10 +32,10 @@ }, "SRR2838702-summary.txt:md5,6f1755af3cdf443a46475b3cac0e37cf", [ - "versions.yml:md5,f0c1c6e03db9f8846867b50f08126e1b" + "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-04-29T11:16:14.368804183", + "timestamp": "2026-07-28T19:40:46.603081275", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/busco/tests/nextflow.config b/modules/busco/tests/nextflow.config index 8231daf08..9dfa990bf 100644 --- a/modules/busco/tests/nextflow.config +++ b/modules/busco/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of BUSCO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/checkm/lineagewf/tests/main.nf.test.snap b/modules/checkm/lineagewf/tests/main.nf.test.snap index 5ab7f5876..3f1a7e305 100644 --- a/modules/checkm/lineagewf/tests/main.nf.test.snap +++ b/modules/checkm/lineagewf/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-04-29T11:25:13.069448253", + "timestamp": "2026-07-28T17:12:42.455049596", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-04-29T11:26:52.020682491", + "timestamp": "2026-07-28T17:14:43.147805748", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm/lineagewf/tests/nextflow.config b/modules/checkm/lineagewf/tests/nextflow.config index 1eb333169..44464ea5d 100644 --- a/modules/checkm/lineagewf/tests/nextflow.config +++ b/modules/checkm/lineagewf/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CHECKM_LINEAGEWF nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/checkm2/predict/tests/main.nf.test.snap b/modules/checkm2/predict/tests/main.nf.test.snap index 760de478b..d9f568359 100644 --- a/modules/checkm2/predict/tests/main.nf.test.snap +++ b/modules/checkm2/predict/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-04-29T11:25:49.447579673", + "timestamp": "2026-07-28T17:13:56.807206506", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-04-29T11:20:50.020786938", + "timestamp": "2026-07-28T17:08:57.106485631", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm2/predict/tests/nextflow.config b/modules/checkm2/predict/tests/nextflow.config index e0a7b1520..2c37e0343 100644 --- a/modules/checkm2/predict/tests/nextflow.config +++ b/modules/checkm2/predict/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CHECKM2_PREDICT nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/clermontyping/tests/main.nf.test.snap b/modules/clermontyping/tests/main.nf.test.snap index ff0dd65af..b4dfde6f9 100644 --- a/modules/clermontyping/tests/main.nf.test.snap +++ b/modules/clermontyping/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-04-29T11:16:43.324300019", + "timestamp": "2026-07-28T17:04:48.741988928", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-04-29T11:16:04.914654129", + "timestamp": "2026-07-28T17:04:11.749476", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clermontyping/tests/nextflow.config b/modules/clermontyping/tests/nextflow.config index c1d01cfad..0acb9da7c 100644 --- a/modules/clermontyping/tests/nextflow.config +++ b/modules/clermontyping/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CLERMONTYPING nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/clonalframeml/tests/main.nf.test.snap b/modules/clonalframeml/tests/main.nf.test.snap index 516ae3021..735271317 100644 --- a/modules/clonalframeml/tests/main.nf.test.snap +++ b/modules/clonalframeml/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-04-29T11:16:42.71640291", + "timestamp": "2026-07-28T17:05:01.420153092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-04-29T11:18:05.517482702", + "timestamp": "2026-07-28T17:06:21.64403345", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clonalframeml/tests/nextflow.config b/modules/clonalframeml/tests/nextflow.config index eb4cce809..e092e8d74 100644 --- a/modules/clonalframeml/tests/nextflow.config +++ b/modules/clonalframeml/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CLONALFRAMEML nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/csvtk/concat/tests/main.nf.test.snap b/modules/csvtk/concat/tests/main.nf.test.snap index bb88d11fa..19d6d1d70 100644 --- a/modules/csvtk/concat/tests/main.nf.test.snap +++ b/modules/csvtk/concat/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-04-29T11:15:38.416605135", + "timestamp": "2026-07-28T17:03:53.009649866", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-04-29T11:15:54.044146975", + "timestamp": "2026-07-28T17:04:06.155187775", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/concat/tests/nextflow.config b/modules/csvtk/concat/tests/nextflow.config index 414ce9b1b..ca5df16f8 100644 --- a/modules/csvtk/concat/tests/nextflow.config +++ b/modules/csvtk/concat/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CSVTK_CONCAT nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/csvtk/join/tests/main.nf.test.snap b/modules/csvtk/join/tests/main.nf.test.snap index 01de082ed..389b58c4e 100644 --- a/modules/csvtk/join/tests/main.nf.test.snap +++ b/modules/csvtk/join/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-04-29T11:15:35.884363273", + "timestamp": "2026-07-28T17:03:47.830304788", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-04-29T11:15:51.646604522", + "timestamp": "2026-07-28T17:04:02.012883981", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/join/tests/nextflow.config b/modules/csvtk/join/tests/nextflow.config index 70642a34a..eb9446b5f 100644 --- a/modules/csvtk/join/tests/nextflow.config +++ b/modules/csvtk/join/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of CSVTK_JOIN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/deacon/fetch/module.config b/modules/deacon/fetch/module.config index e22861783..0f4a33f38 100644 --- a/modules/deacon/fetch/module.config +++ b/modules/deacon/fetch/module.config @@ -1,7 +1,7 @@ params { // deacon_fetch - deacon_index_name = "panhuman-1" deacon_db = null + deacon_index_name = "panhuman-1" download_deacon = false use_deacon = false } diff --git a/modules/deacon/filter/main.nf b/modules/deacon/filter/main.nf index 2c64148bf..c084e66f2 100644 --- a/modules/deacon/filter/main.nf +++ b/modules/deacon/filter/main.nf @@ -24,13 +24,14 @@ * @input db * Deacon minimizer index file (.idx) for host read filtering * - * @output record(meta, special_meta, r1?, r2?, se?, lr?, scrub_report, results, logs, nf_logs, versions) + * @output record(meta, special_meta, r1?, r2?, se?, lr?, scrub_report, json_summary, results, logs, nf_logs, versions) * - `special_meta`: A simplified metadata record for downstream report joining * - `r1?`: Filtered paired-end forward reads * - `r2?`: Filtered paired-end reverse reads * - `se?`: Filtered single-end reads * - `lr?`: Filtered long reads * - `scrub_report`: Summary report of reads removed during filtering + * - `json_summary`: Deacon JSON summary of the filtering run */ nextflow.enable.types = true diff --git a/modules/deacon/filter/tests/main.nf.test.snap b/modules/deacon/filter/tests/main.nf.test.snap index 703cfb7b5..419b5fbba 100644 --- a/modules/deacon/filter/tests/main.nf.test.snap +++ b/modules/deacon/filter/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-05-06T14:35:01.429376554", + "timestamp": "2026-07-28T17:05:10.605107483", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-05-06T14:34:44.548001567", + "timestamp": "2026-07-28T17:04:35.120671774", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-05-06T14:34:29.120029938", + "timestamp": "2026-07-28T17:04:02.976247105", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/deacon/filter/tests/nextflow.config b/modules/deacon/filter/tests/nextflow.config index 642d3e944..88de10025 100644 --- a/modules/deacon/filter/tests/nextflow.config +++ b/modules/deacon/filter/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of DEACON_FILTER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/defensefinder/run/module.config b/modules/defensefinder/run/module.config index d4eaa35a5..1aa5002f8 100644 --- a/modules/defensefinder/run/module.config +++ b/modules/defensefinder/run/module.config @@ -23,9 +23,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::defense-finder=2.0.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/defense-finder:2.0.1--pyhdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/defense-finder:2.0.1--pyhdfd78af_0" + ext.toolName = "bioconda::defense-finder=3.0.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/defense-finder:3.0.0--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/defense-finder:3.0.0--pyhdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/defensefinder/run/tests/main.nf.test.snap b/modules/defensefinder/run/tests/main.nf.test.snap index 7ca2d4159..15b335f5a 100644 --- a/modules/defensefinder/run/tests/main.nf.test.snap +++ b/modules/defensefinder/run/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,96378138554cc40b07841aed5efb3e7d" ] ], - "timestamp": "2026-04-29T11:16:13.441035414", + "timestamp": "2026-07-28T17:04:31.48211912", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/defensefinder/run/tests/nextflow.config b/modules/defensefinder/run/tests/nextflow.config index 0e4f33ae6..f9434ab27 100644 --- a/modules/defensefinder/run/tests/nextflow.config +++ b/modules/defensefinder/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of DEFENSEFINDER_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/defensefinder/update/module.config b/modules/defensefinder/update/module.config index 900a19249..9ac900008 100644 --- a/modules/defensefinder/update/module.config +++ b/modules/defensefinder/update/module.config @@ -15,9 +15,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::defense-finder=2.0.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/defense-finder:2.0.1--pyhdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/defense-finder:2.0.1--pyhdfd78af_0" + ext.toolName = "bioconda::defense-finder=3.0.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/defense-finder:3.0.0--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/defense-finder:3.0.0--pyhdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/defensefinder/update/tests/nextflow.config b/modules/defensefinder/update/tests/nextflow.config index 88f400f3f..d11726604 100644 --- a/modules/defensefinder/update/tests/nextflow.config +++ b/modules/defensefinder/update/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of DEFENSEFINDER_UPDATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/ectyper/tests/main.nf.test.snap b/modules/ectyper/tests/main.nf.test.snap index e721d41a0..5ee290000 100644 --- a/modules/ectyper/tests/main.nf.test.snap +++ b/modules/ectyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-04-29T11:16:38.699285839", + "timestamp": "2026-07-28T17:05:03.748844858", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-04-29T11:15:59.994882882", + "timestamp": "2026-07-28T17:04:23.970768955", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ectyper/tests/nextflow.config b/modules/ectyper/tests/nextflow.config index b60a37ebd..efa80ab38 100644 --- a/modules/ectyper/tests/nextflow.config +++ b/modules/ectyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ECTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/eggnog/download/module.config b/modules/eggnog/download/module.config index b17130859..a787616c7 100644 --- a/modules/eggnog/download/module.config +++ b/modules/eggnog/download/module.config @@ -32,9 +32,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::eggnog-mapper=2.1.13".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/eggnog-mapper:2.1.13--pyhdfd78af_2" - ext.image = "https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.13--pyhdfd78af_2" + ext.toolName = "bioconda::eggnog-mapper=2.1.15".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/eggnog-mapper:2.1.15--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.15--pyhdfd78af_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/eggnog/mapper/module.config b/modules/eggnog/mapper/module.config index d13488fa2..692811472 100644 --- a/modules/eggnog/mapper/module.config +++ b/modules/eggnog/mapper/module.config @@ -21,9 +21,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::eggnog-mapper=2.1.13".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/eggnog-mapper:2.1.13--pyhdfd78af_2" - ext.image = "https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.13--pyhdfd78af_2" + ext.toolName = "bioconda::eggnog-mapper=2.1.15".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/eggnog-mapper:2.1.15--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.15--pyhdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/eggnog/mapper/tests/main.nf.test.snap b/modules/eggnog/mapper/tests/main.nf.test.snap index b247c7e47..6c9bce1ec 100644 --- a/modules/eggnog/mapper/tests/main.nf.test.snap +++ b/modules/eggnog/mapper/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "sample" }, [ - "versions.yml:md5,2784870d86d92b80930b2cc28c81757d" + "versions.yml:md5,591b018c5d70f26267582a8932b0271d" ] ], - "timestamp": "2026-04-29T11:29:26.491545586", + "timestamp": "2026-07-28T17:17:26.374518532", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -30,10 +30,10 @@ "scope": "sample" }, [ - "versions.yml:md5,2784870d86d92b80930b2cc28c81757d" + "versions.yml:md5,591b018c5d70f26267582a8932b0271d" ] ], - "timestamp": "2026-04-29T11:33:43.79747669", + "timestamp": "2026-07-28T17:21:41.280155523", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/eggnog/mapper/tests/nextflow.config b/modules/eggnog/mapper/tests/nextflow.config index c11fe59be..9a7b70a18 100644 --- a/modules/eggnog/mapper/tests/nextflow.config +++ b/modules/eggnog/mapper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of EGGNOG_MAPPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,10 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 12 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/emmtyper/tests/main.nf.test.snap b/modules/emmtyper/tests/main.nf.test.snap index 00b20c4a6..60bfa469f 100644 --- a/modules/emmtyper/tests/main.nf.test.snap +++ b/modules/emmtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-04-29T11:15:48.369769489", + "timestamp": "2026-07-28T17:04:16.232229719", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-04-29T11:16:04.878639906", + "timestamp": "2026-07-28T17:04:33.141894812", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-04-29T11:15:33.033869822", + "timestamp": "2026-07-28T17:03:59.67691452", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/emmtyper/tests/nextflow.config b/modules/emmtyper/tests/nextflow.config index f50a8a422..45d8d006c 100644 --- a/modules/emmtyper/tests/nextflow.config +++ b/modules/emmtyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of EMMTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/fastani/tests/main.nf.test.snap b/modules/fastani/tests/main.nf.test.snap index ca676021b..9bf90a5ab 100644 --- a/modules/fastani/tests/main.nf.test.snap +++ b/modules/fastani/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-04-29T11:15:33.056261848", + "timestamp": "2026-07-28T17:03:48.547821427", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-04-29T11:15:47.327096724", + "timestamp": "2026-07-28T17:04:03.686628869", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/fastani/tests/nextflow.config b/modules/fastani/tests/nextflow.config index cc37ece27..f88211325 100644 --- a/modules/fastani/tests/nextflow.config +++ b/modules/fastani/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of FASTANI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/gamma/tests/main.nf.test.snap b/modules/gamma/tests/main.nf.test.snap index 4c0f3100c..20750d6d1 100644 --- a/modules/gamma/tests/main.nf.test.snap +++ b/modules/gamma/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-04-29T11:15:41.617890697", + "timestamp": "2026-07-28T17:03:51.924823231", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-04-29T11:15:58.34573894", + "timestamp": "2026-07-28T17:04:05.726715129", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gamma/tests/nextflow.config b/modules/gamma/tests/nextflow.config index 7e010b4b4..8c54d1aec 100644 --- a/modules/gamma/tests/nextflow.config +++ b/modules/gamma/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GAMMA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/genomedl/tests/main.nf.test.snap b/modules/genomedl/tests/main.nf.test.snap index 21a1d2376..874a2d322 100644 --- a/modules/genomedl/tests/main.nf.test.snap +++ b/modules/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-27T10:23:32.083383414", + "timestamp": "2026-07-28T17:04:12.889654592", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-27T10:23:24.497928112", + "timestamp": "2026-07-28T17:03:54.906366097", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-27T10:23:39.277366568", + "timestamp": "2026-07-28T17:04:29.596345709", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genomedl/tests/nextflow.config b/modules/genomedl/tests/nextflow.config index c8dece7a8..87708b3cb 100644 --- a/modules/genomedl/tests/nextflow.config +++ b/modules/genomedl/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GENOMEDL nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/genotyphi/parse/tests/main.nf.test.snap b/modules/genotyphi/parse/tests/main.nf.test.snap index e1416d707..59995b02c 100644 --- a/modules/genotyphi/parse/tests/main.nf.test.snap +++ b/modules/genotyphi/parse/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,359680888d6e4e84784879e6e92c3439" ] ], - "timestamp": "2026-04-29T11:15:36.410818766", + "timestamp": "2026-07-28T17:03:53.300346668", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genotyphi/parse/tests/nextflow.config b/modules/genotyphi/parse/tests/nextflow.config index 286ee6d70..645c31754 100644 --- a/modules/genotyphi/parse/tests/nextflow.config +++ b/modules/genotyphi/parse/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GENOTYPHI_PARSE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/gigatyper/tests/main.nf.test.snap b/modules/gigatyper/tests/main.nf.test.snap index 8a85cf33c..bd55af5dc 100644 --- a/modules/gigatyper/tests/main.nf.test.snap +++ b/modules/gigatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ae98787b0c6ddf8f10515b895570a41a" ] ], - "timestamp": "2026-04-29T11:15:49.784505502", + "timestamp": "2026-07-28T17:04:03.754486026", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gigatyper/tests/nextflow.config b/modules/gigatyper/tests/nextflow.config index 693decf6b..d10847f05 100644 --- a/modules/gigatyper/tests/nextflow.config +++ b/modules/gigatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GIGATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/gtdbtk/classifywf/module.config b/modules/gtdbtk/classifywf/module.config index 77ebdc0da..ac2884178 100644 --- a/modules/gtdbtk/classifywf/module.config +++ b/modules/gtdbtk/classifywf/module.config @@ -30,9 +30,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::gtdbtk=2.7.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/gtdbtk:2.7.1--pyhdfd78af_1" - ext.image = "https://depot.galaxyproject.org/singularity/gtdbtk:2.7.1--pyhdfd78af_1" + ext.toolName = "bioconda::gtdbtk=2.7.2".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/gtdbtk:2.7.2--pyhdfd78af_1" + ext.image = "https://depot.galaxyproject.org/singularity/gtdbtk:2.7.2--pyhdfd78af_1" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/gtdbtk/classifywf/tests/main.nf.test.snap index d70bfac68..7c62a9468 100644 --- a/modules/gtdbtk/classifywf/tests/main.nf.test.snap +++ b/modules/gtdbtk/classifywf/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "sample" }, [ - "versions.yml:md5,f023d15f8b26e9599946afeb72989b98" + "versions.yml:md5,7cb27f0b82d34e40565279ff91f60fda" ] ], - "timestamp": "2026-04-29T11:20:34.013534922", + "timestamp": "2026-07-28T17:08:44.100864413", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gtdbtk/classifywf/tests/nextflow.config b/modules/gtdbtk/classifywf/tests/nextflow.config index 5bd46b0d4..7eb03e6e9 100644 --- a/modules/gtdbtk/classifywf/tests/nextflow.config +++ b/modules/gtdbtk/classifywf/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GTDBTK_CLASSIFYWF nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,26 +11,12 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h max_memory = 144.GB max_cpus = 32 - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - // GTDB-Tk specific run_name = "" } diff --git a/modules/gtdbtk/download/module.config b/modules/gtdbtk/download/module.config index 8d22de7d9..f2a8cd46d 100644 --- a/modules/gtdbtk/download/module.config +++ b/modules/gtdbtk/download/module.config @@ -23,9 +23,9 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::gtdbtk=2.7.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/gtdbtk:2.7.1--pyhdfd78af_1" - ext.image = "https://depot.galaxyproject.org/singularity/gtdbtk:2.7.1--pyhdfd78af_1" + ext.toolName = "bioconda::gtdbtk=2.7.2".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/gtdbtk:2.7.2--pyhdfd78af_1" + ext.image = "https://depot.galaxyproject.org/singularity/gtdbtk:2.7.2--pyhdfd78af_1" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/gubbins/tests/main.nf.test.snap b/modules/gubbins/tests/main.nf.test.snap index f60c90555..c13623d80 100644 --- a/modules/gubbins/tests/main.nf.test.snap +++ b/modules/gubbins/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-04-29T11:15:53.545814148", + "timestamp": "2026-07-28T17:04:08.285562828", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-04-29T11:16:30.454810404", + "timestamp": "2026-07-28T17:04:45.743885757", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gubbins/tests/nextflow.config b/modules/gubbins/tests/nextflow.config index 10642aac1..e5c52811e 100644 --- a/modules/gubbins/tests/nextflow.config +++ b/modules/gubbins/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of GUBBINS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,10 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 4 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/hicap/tests/main.nf.test.snap b/modules/hicap/tests/main.nf.test.snap index a6cb5c1bd..f76edd6bd 100644 --- a/modules/hicap/tests/main.nf.test.snap +++ b/modules/hicap/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-04-29T11:16:38.289081697", + "timestamp": "2026-07-28T17:05:05.438707309", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-04-29T11:15:56.229487967", + "timestamp": "2026-07-28T17:04:23.651765181", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-04-29T11:17:56.200188445", + "timestamp": "2026-07-28T17:06:19.426592773", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-04-29T11:17:16.975963914", + "timestamp": "2026-07-28T17:05:43.02612693", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hicap/tests/nextflow.config b/modules/hicap/tests/nextflow.config index 6338272b9..06ece62c9 100644 --- a/modules/hicap/tests/nextflow.config +++ b/modules/hicap/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of HICAP nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/hpsuissero/tests/main.nf.test.snap b/modules/hpsuissero/tests/main.nf.test.snap index 06694c9a8..85ae7eecd 100644 --- a/modules/hpsuissero/tests/main.nf.test.snap +++ b/modules/hpsuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-04-29T11:15:55.922851305", + "timestamp": "2026-07-28T17:04:15.224903196", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-04-29T11:15:39.077032116", + "timestamp": "2026-07-28T17:03:59.195283123", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hpsuissero/tests/nextflow.config b/modules/hpsuissero/tests/nextflow.config index a9430ab8c..e0622e8b4 100644 --- a/modules/hpsuissero/tests/nextflow.config +++ b/modules/hpsuissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of HPSUISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/iqtree/module.config b/modules/iqtree/module.config index 4027f9cb7..89577255b 100644 --- a/modules/iqtree/module.config +++ b/modules/iqtree/module.config @@ -26,9 +26,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::iqtree=3.1.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/iqtree:3.1.1--hde5307d_1" - ext.image = "https://depot.galaxyproject.org/singularity/iqtree:3.1.1--hde5307d_1" + ext.toolName = "bioconda::iqtree=3.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/iqtree:3.1.3--h8471819_0" + ext.image = "https://depot.galaxyproject.org/singularity/iqtree:3.1.3--h8471819_0" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/iqtree/tests/main.nf.test.snap b/modules/iqtree/tests/main.nf.test.snap index 9bacc751c..ee623057c 100644 --- a/modules/iqtree/tests/main.nf.test.snap +++ b/modules/iqtree/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "run" }, [ - "versions.yml:md5,7c9654347c5eee68869012773f03db28" + "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-04-29T11:15:58.939802654", + "timestamp": "2026-07-28T17:04:22.270835292", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -30,10 +30,10 @@ "scope": "run" }, [ - "versions.yml:md5,7c9654347c5eee68869012773f03db28" + "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-04-29T11:15:42.55950921", + "timestamp": "2026-07-28T17:04:06.216512741", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/iqtree/tests/nextflow.config b/modules/iqtree/tests/nextflow.config index d21a37758..2cd1f2427 100644 --- a/modules/iqtree/tests/nextflow.config +++ b/modules/iqtree/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of IQTREE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/ismapper/tests/main.nf.test.snap b/modules/ismapper/tests/main.nf.test.snap index 643a482e8..c22cfca05 100644 --- a/modules/ismapper/tests/main.nf.test.snap +++ b/modules/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,bbe2280116459026bfc2304b2b6c0f5f" ] ], - "timestamp": "2026-04-29T11:16:35.274177837", + "timestamp": "2026-07-28T17:04:48.918091806", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ismapper/tests/nextflow.config b/modules/ismapper/tests/nextflow.config index 358fe7bf4..5fc772ecd 100644 --- a/modules/ismapper/tests/nextflow.config +++ b/modules/ismapper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ISMAPPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/kleborate/tests/main.nf.test.snap b/modules/kleborate/tests/main.nf.test.snap index 60f2bccc4..997a491b0 100644 --- a/modules/kleborate/tests/main.nf.test.snap +++ b/modules/kleborate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9511fd36659702fc20722109151dca4b" ] ], - "timestamp": "2026-04-29T11:16:02.985211375", + "timestamp": "2026-07-28T17:04:28.2033193", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kleborate/tests/nextflow.config b/modules/kleborate/tests/nextflow.config index 3f8abc7ad..cab43b0da 100644 --- a/modules/kleborate/tests/nextflow.config +++ b/modules/kleborate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of KLEBORATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/kraken2/tests/main.nf.test.snap b/modules/kraken2/tests/main.nf.test.snap index 0bd8f25c2..565b8164f 100644 --- a/modules/kraken2/tests/main.nf.test.snap +++ b/modules/kraken2/tests/main.nf.test.snap @@ -11,10 +11,10 @@ "single_end": false }, [ - "versions.yml:md5,f9292e3762a8b98912643f1c044b07f2" + "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-04-29T11:19:46.509803138", + "timestamp": "2026-07-28T17:10:02.058157343", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -32,10 +32,10 @@ "single_end": false }, [ - "versions.yml:md5,f9292e3762a8b98912643f1c044b07f2" + "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-04-29T11:15:56.544183038", + "timestamp": "2026-07-28T17:04:05.745055868", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kraken2/tests/nextflow.config b/modules/kraken2/tests/nextflow.config index 7e595da0e..a786a89c3 100644 --- a/modules/kraken2/tests/nextflow.config +++ b/modules/kraken2/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of KRAKEN2 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/legsta/tests/main.nf.test.snap b/modules/legsta/tests/main.nf.test.snap index d763204bd..25421029e 100644 --- a/modules/legsta/tests/main.nf.test.snap +++ b/modules/legsta/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1ea80a08aa0a9efc6d82ffa9e668ad6d" ] ], - "timestamp": "2026-04-29T11:15:32.144911959", + "timestamp": "2026-07-28T17:03:49.761469566", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/legsta/tests/nextflow.config b/modules/legsta/tests/nextflow.config index e1876d69e..aa4fafff2 100644 --- a/modules/legsta/tests/nextflow.config +++ b/modules/legsta/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of LEGSTA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/lissero/tests/main.nf.test.snap b/modules/lissero/tests/main.nf.test.snap index a61fc1ea2..706772e8b 100644 --- a/modules/lissero/tests/main.nf.test.snap +++ b/modules/lissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-04-29T11:15:50.368192123", + "timestamp": "2026-07-28T17:04:19.361243979", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-04-29T11:15:33.497457272", + "timestamp": "2026-07-28T17:04:02.075983877", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/lissero/tests/nextflow.config b/modules/lissero/tests/nextflow.config index d08382ca5..42cf4b4ea 100644 --- a/modules/lissero/tests/nextflow.config +++ b/modules/lissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of LISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/mash/dist/module.config b/modules/mash/dist/module.config index d4202d012..e62d0b6ea 100644 --- a/modules/mash/dist/module.config +++ b/modules/mash/dist/module.config @@ -31,8 +31,8 @@ process { // Environment information ext.toolName = "bioconda::mash=2.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/mash:2.3--hb105d93_10" - ext.image = "https://depot.galaxyproject.org/singularity/mash:2.3--hb105d93_10" + ext.docker = "biocontainers/mash:2.3--hf85e966_11" + ext.image = "https://depot.galaxyproject.org/singularity/mash:2.3--hf85e966_11" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/mash/dist/tests/main.nf.test.snap b/modules/mash/dist/tests/main.nf.test.snap index d4e7e2d0d..b2b1dd1d5 100644 --- a/modules/mash/dist/tests/main.nf.test.snap +++ b/modules/mash/dist/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-04-29T11:15:44.358692007", + "timestamp": "2026-07-28T17:04:09.318813499", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-04-29T11:15:30.968891098", + "timestamp": "2026-07-28T17:03:54.746407145", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mash/dist/tests/nextflow.config b/modules/mash/dist/tests/nextflow.config index e65ef262f..4a3ca7606 100644 --- a/modules/mash/dist/tests/nextflow.config +++ b/modules/mash/dist/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MASH_DIST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Mash dist specific ask_merlin = false diff --git a/modules/mashtree/tests/main.nf.test.snap b/modules/mashtree/tests/main.nf.test.snap index 0c6269d7d..1fdd9afcb 100644 --- a/modules/mashtree/tests/main.nf.test.snap +++ b/modules/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,6d51bcb025e39e73864f2236b1ce99e9" ] ], - "timestamp": "2026-04-29T11:15:33.989920095", + "timestamp": "2026-07-28T17:03:51.860130438", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mashtree/tests/nextflow.config b/modules/mashtree/tests/nextflow.config index 5a4af57a6..25083a1f9 100644 --- a/modules/mashtree/tests/nextflow.config +++ b/modules/mashtree/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MASHTREE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/mcroni/tests/main.nf.test.snap b/modules/mcroni/tests/main.nf.test.snap index f290192e3..856b55cea 100644 --- a/modules/mcroni/tests/main.nf.test.snap +++ b/modules/mcroni/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-04-29T11:15:46.785524863", + "timestamp": "2026-07-28T17:04:12.006871014", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-04-29T11:15:32.422346592", + "timestamp": "2026-07-28T17:03:55.324984592", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mcroni/tests/nextflow.config b/modules/mcroni/tests/nextflow.config index 5112d5baa..e4cf2bd01 100644 --- a/modules/mcroni/tests/nextflow.config +++ b/modules/mcroni/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MCRONI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/meningotype/tests/main.nf.test.snap b/modules/meningotype/tests/main.nf.test.snap index 767904f13..a3942cde4 100644 --- a/modules/meningotype/tests/main.nf.test.snap +++ b/modules/meningotype/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-04-29T11:15:48.022863891", + "timestamp": "2026-07-28T17:04:10.175706031", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-04-29T11:15:31.953507021", + "timestamp": "2026-07-28T17:03:53.421375832", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/meningotype/tests/nextflow.config b/modules/meningotype/tests/nextflow.config index eac4673ae..7425e0cd4 100644 --- a/modules/meningotype/tests/nextflow.config +++ b/modules/meningotype/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MENINGOTYPE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/merlin/dist/module.config b/modules/merlin/dist/module.config index 6f0f85142..53661fa97 100644 --- a/modules/merlin/dist/module.config +++ b/modules/merlin/dist/module.config @@ -32,8 +32,8 @@ process { // Environment information ext.toolName = "bioconda::mash=2.3".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/mash:2.3--hb105d93_10" - ext.image = "https://depot.galaxyproject.org/singularity/mash:2.3--hb105d93_10" + ext.docker = "biocontainers/mash:2.3--hf85e966_11" + ext.image = "https://depot.galaxyproject.org/singularity/mash:2.3--hf85e966_11" ext.condaDir = "${params.condadir}" // Module-specific parameters diff --git a/modules/merlin/dist/tests/main.nf.test.snap b/modules/merlin/dist/tests/main.nf.test.snap index 71b190d8a..b6ec83a0b 100644 --- a/modules/merlin/dist/tests/main.nf.test.snap +++ b/modules/merlin/dist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-04-29T11:16:56.070387534", + "timestamp": "2026-07-28T17:05:05.379345937", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-04-29T11:18:20.752298012", + "timestamp": "2026-07-28T17:06:25.456477033", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/merlin/dist/tests/nextflow.config b/modules/merlin/dist/tests/nextflow.config index 698bbde6e..7849216f7 100644 --- a/modules/merlin/dist/tests/nextflow.config +++ b/modules/merlin/dist/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MERLIN_DIST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,27 +11,9 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true run_name = "merlin" ask_merlin = false - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/midas/species/tests/main.nf.test.snap b/modules/midas/species/tests/main.nf.test.snap index beb2ceb4b..d6b2485ec 100644 --- a/modules/midas/species/tests/main.nf.test.snap +++ b/modules/midas/species/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-04-29T11:22:53.910500819", + "timestamp": "2026-07-28T17:10:58.232093107", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-04-29T11:23:48.2696469", + "timestamp": "2026-07-28T17:11:55.860507334", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/midas/species/tests/nextflow.config b/modules/midas/species/tests/nextflow.config index 7e4e15ef0..b98135c78 100644 --- a/modules/midas/species/tests/nextflow.config +++ b/modules/midas/species/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MIDAS_SPECIES nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/mlst/module.config b/modules/mlst/module.config index c613b3609..2517ef7ed 100644 --- a/modules/mlst/module.config +++ b/modules/mlst/module.config @@ -26,9 +26,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::mlst=2.33.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/mlst:2.33.1--hdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/mlst:2.33.1--hdfd78af_0" + ext.toolName = "bioconda::mlst=2.35.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/mlst:2.35.0--hdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/mlst:2.35.0--hdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/mlst/tests/main.nf.test.snap b/modules/mlst/tests/main.nf.test.snap index 0f3cee432..977b49d95 100644 --- a/modules/mlst/tests/main.nf.test.snap +++ b/modules/mlst/tests/main.nf.test.snap @@ -11,10 +11,10 @@ }, "GCF_000017085.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6", [ - "versions.yml:md5,430105b9f7348fc38a47d20c19daf7fd" + "versions.yml:md5,6515f9242cdb83b9c720f39ce67a528f" ] ], - "timestamp": "2026-04-29T11:15:42.575237329", + "timestamp": "2026-07-28T17:03:51.417063793", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mlst/tests/nextflow.config b/modules/mlst/tests/nextflow.config index f868d0310..1da3f8424 100644 --- a/modules/mlst/tests/nextflow.config +++ b/modules/mlst/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MLST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/mobsuite/recon/tests/main.nf.test.snap b/modules/mobsuite/recon/tests/main.nf.test.snap index f551a776e..4dbbdfd2b 100644 --- a/modules/mobsuite/recon/tests/main.nf.test.snap +++ b/modules/mobsuite/recon/tests/main.nf.test.snap @@ -18,10 +18,10 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-27T16:45:56.17998057", + "timestamp": "2026-07-28T17:07:55.232262612", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.0" } }, "mobsuite_recon - module - GCF_000017085 - compressed": { @@ -40,7 +40,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-04-29T11:18:35.704802529", + "timestamp": "2026-07-28T17:06:46.930322714", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-04-29T11:16:55.889054755", + "timestamp": "2026-07-28T17:05:12.990479906", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mobsuite/recon/tests/nextflow.config b/modules/mobsuite/recon/tests/nextflow.config index 8f1b94a7b..3da4fdba1 100644 --- a/modules/mobsuite/recon/tests/nextflow.config +++ b/modules/mobsuite/recon/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MOBSUITE_RECON nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/mykrobe/predict/tests/main.nf.test.snap b/modules/mykrobe/predict/tests/main.nf.test.snap index 88e19458b..e1b4fc2e7 100644 --- a/modules/mykrobe/predict/tests/main.nf.test.snap +++ b/modules/mykrobe/predict/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,3756fdfbed62cef8782098468ef3da9d" ] ], - "timestamp": "2026-04-29T11:15:40.218598288", + "timestamp": "2026-07-28T17:03:59.629821371", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mykrobe/predict/tests/nextflow.config b/modules/mykrobe/predict/tests/nextflow.config index a2633eee2..9006a0321 100644 --- a/modules/mykrobe/predict/tests/nextflow.config +++ b/modules/mykrobe/predict/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of MYKROBE_PREDICT nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/ngmaster/module.config b/modules/ngmaster/module.config index da92118b2..54e483a3c 100644 --- a/modules/ngmaster/module.config +++ b/modules/ngmaster/module.config @@ -17,9 +17,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::ngmaster=2.0.0".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/ngmaster:2.0.0--pyhdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/ngmaster:2.0.0--pyhdfd78af_0" + ext.toolName = "bioconda::ngmaster=2.1.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/ngmaster:2.1.0--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/ngmaster:2.1.0--pyhdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/ngmaster/tests/main.nf.test.snap b/modules/ngmaster/tests/main.nf.test.snap index 2a4b317b3..bbeeb6cf3 100644 --- a/modules/ngmaster/tests/main.nf.test.snap +++ b/modules/ngmaster/tests/main.nf.test.snap @@ -11,10 +11,10 @@ }, "GCF_001047255.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219", [ - "versions.yml:md5,141b09741c21ba1bdf441bfba28bbfa9" + "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-04-29T11:15:47.027126264", + "timestamp": "2026-07-28T17:03:53.644612074", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -32,10 +32,10 @@ }, "GCF_001047255.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219", [ - "versions.yml:md5,141b09741c21ba1bdf441bfba28bbfa9" + "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-04-29T11:16:23.109381544", + "timestamp": "2026-07-28T17:04:15.788207516", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ngmaster/tests/nextflow.config b/modules/ngmaster/tests/nextflow.config index 86ea7a804..3136e325a 100644 --- a/modules/ngmaster/tests/nextflow.config +++ b/modules/ngmaster/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of NGMASTER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/nohuman/download/module.config b/modules/nohuman/download/module.config index 1050d69d7..cc453ec8e 100644 --- a/modules/nohuman/download/module.config +++ b/modules/nohuman/download/module.config @@ -2,9 +2,9 @@ params { // nohuman_download download_nohuman = false nohuman_db = null - use_nohuman = false nohuman_db_version = "" nohuman_save_as_tarball = false + use_nohuman = false } process { diff --git a/modules/nohuman/run/tests/main.nf.test.snap b/modules/nohuman/run/tests/main.nf.test.snap index 16e6259b3..74637d4f0 100644 --- a/modules/nohuman/run/tests/main.nf.test.snap +++ b/modules/nohuman/run/tests/main.nf.test.snap @@ -16,10 +16,10 @@ }, "SRR2838702.scrub.report.tsv:md5,4b0dcd803f7da2cc2d79b8cc5cac403c", [ - "versions.yml:md5,12c5ca2725279a466f337e5a5de7b27b" + "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-04-29T11:26:46.3896525", + "timestamp": "2026-07-28T17:15:29.132571832", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -42,10 +42,10 @@ }, "SRR2838702.scrub.report.tsv:md5,0bc664ae0be37cb6ebd8490f3a11f973", [ - "versions.yml:md5,12c5ca2725279a466f337e5a5de7b27b" + "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-04-29T11:30:23.430469379", + "timestamp": "2026-07-28T17:19:06.11822473", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -68,10 +68,10 @@ }, "SRR2838702.scrub.report.tsv:md5,4b0dcd803f7da2cc2d79b8cc5cac403c", [ - "versions.yml:md5,12c5ca2725279a466f337e5a5de7b27b" + "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-04-29T11:22:42.057476779", + "timestamp": "2026-07-28T17:10:47.757626415", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/nohuman/run/tests/nextflow.config b/modules/nohuman/run/tests/nextflow.config index cfa8f6137..98eddee1f 100644 --- a/modules/nohuman/run/tests/nextflow.config +++ b/modules/nohuman/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of NOHUMAN_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/panaroo/run/module.config b/modules/panaroo/run/module.config index cfde06451..2df7a2d0d 100644 --- a/modules/panaroo/run/module.config +++ b/modules/panaroo/run/module.config @@ -33,9 +33,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::panaroo=1.6.0".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/panaroo:1.6.0--pyhdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/panaroo:1.6.0--pyhdfd78af_0" + ext.toolName = "bioconda::panaroo=1.8.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/panaroo:1.8.0--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/panaroo:1.8.0--pyhdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/panaroo/run/tests/main.nf.test.snap b/modules/panaroo/run/tests/main.nf.test.snap index bc2b39f8f..f10e6e127 100644 --- a/modules/panaroo/run/tests/main.nf.test.snap +++ b/modules/panaroo/run/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "run" }, [ - "versions.yml:md5,bc3e44bf3b11c0eddd36a31af1aa71a4" + "versions.yml:md5,e6a0f1e191dcfb92fab2a7d68063c31d" ] ], - "timestamp": "2026-04-29T11:17:35.290114895", + "timestamp": "2026-07-28T19:41:35.651447042", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/panaroo/run/tests/nextflow.config b/modules/panaroo/run/tests/nextflow.config index e8b6438e4..7ba79dc01 100644 --- a/modules/panaroo/run/tests/nextflow.config +++ b/modules/panaroo/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PANAROO_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/pasty/tests/main.nf.test.snap b/modules/pasty/tests/main.nf.test.snap index e6d82f6a3..b7d6eb68b 100644 --- a/modules/pasty/tests/main.nf.test.snap +++ b/modules/pasty/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,275841ecfb594907dd941a31a5e5f171" ] ], - "timestamp": "2026-04-29T11:15:36.307925094", + "timestamp": "2026-07-28T17:04:01.864693232", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pasty/tests/nextflow.config b/modules/pasty/tests/nextflow.config index d1160e619..312c7d295 100644 --- a/modules/pasty/tests/nextflow.config +++ b/modules/pasty/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PASTY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/pbptyper/tests/main.nf.test.snap b/modules/pbptyper/tests/main.nf.test.snap index 8f849b077..b15a9bac3 100644 --- a/modules/pbptyper/tests/main.nf.test.snap +++ b/modules/pbptyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,be74af83bdcf74f71056df98990fdeda" ] ], - "timestamp": "2026-04-29T11:16:10.533716034", + "timestamp": "2026-07-28T17:04:40.027774057", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pbptyper/tests/nextflow.config b/modules/pbptyper/tests/nextflow.config index 4c0b7c705..be4072281 100644 --- a/modules/pbptyper/tests/nextflow.config +++ b/modules/pbptyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PBPTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/phispy/module.config b/modules/phispy/module.config index 6215a7664..aca74c1e7 100644 --- a/modules/phispy/module.config +++ b/modules/phispy/module.config @@ -29,9 +29,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::phispy=5.0.6".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/phispy:5.0.6--py311h483b626_0" - ext.image = "https://depot.galaxyproject.org/singularity/phispy:5.0.6--py311h483b626_0" + ext.toolName = "bioconda::phispy=5.0.10".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/phispy:5.0.10--py311h0e292b2_0" + ext.image = "https://depot.galaxyproject.org/singularity/phispy:5.0.10--py311h0e292b2_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/phispy/tests/main.nf.test.snap b/modules/phispy/tests/main.nf.test.snap index 2a3d1d966..b5a1c54b8 100644 --- a/modules/phispy/tests/main.nf.test.snap +++ b/modules/phispy/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "sample" }, [ - "versions.yml:md5,5d58358ef1d0dba349319f20bc5c1602" + "versions.yml:md5,97542c4eb1d90b2b0a0375c916b75dc5" ] ], - "timestamp": "2026-04-29T11:18:13.916716092", + "timestamp": "2026-07-28T17:06:15.020944732", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/phispy/tests/nextflow.config b/modules/phispy/tests/nextflow.config index 1de465e6a..fac8960b7 100644 --- a/modules/phispy/tests/nextflow.config +++ b/modules/phispy/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PHISPY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/pirate/tests/main.nf.test.snap b/modules/pirate/tests/main.nf.test.snap index b18f1acb0..03b5e4f78 100644 --- a/modules/pirate/tests/main.nf.test.snap +++ b/modules/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,ce4d40e2b87e2e5cac6e755fcb0c023b" ] ], - "timestamp": "2026-04-29T11:19:02.881672069", + "timestamp": "2026-07-28T17:07:05.838150755", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pirate/tests/nextflow.config b/modules/pirate/tests/nextflow.config index 7fca74bff..f93c8a481 100644 --- a/modules/pirate/tests/nextflow.config +++ b/modules/pirate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PIRATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/plasmidfinder/tests/main.nf.test.snap b/modules/plasmidfinder/tests/main.nf.test.snap index 369890b85..6cf93371a 100644 --- a/modules/plasmidfinder/tests/main.nf.test.snap +++ b/modules/plasmidfinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-04-29T11:15:48.064199264", + "timestamp": "2026-07-28T17:04:09.34637667", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-04-29T11:16:10.853956728", + "timestamp": "2026-07-28T17:04:31.879284068", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/plasmidfinder/tests/nextflow.config b/modules/plasmidfinder/tests/nextflow.config index ae6679b46..09cfcd577 100644 --- a/modules/plasmidfinder/tests/nextflow.config +++ b/modules/plasmidfinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PLASMIDFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/pneumocat/tests/main.nf.test.snap b/modules/pneumocat/tests/main.nf.test.snap index 1705b880b..7c2aa5ba9 100644 --- a/modules/pneumocat/tests/main.nf.test.snap +++ b/modules/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf" ] ], - "timestamp": "2026-04-29T11:16:11.042825354", + "timestamp": "2026-07-28T17:04:10.996091644", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pneumocat/tests/nextflow.config b/modules/pneumocat/tests/nextflow.config index f07b67537..290830ef6 100644 --- a/modules/pneumocat/tests/nextflow.config +++ b/modules/pneumocat/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PNEUMOCAT nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/prokka/tests/main.nf.test.snap b/modules/prokka/tests/main.nf.test.snap index 1d3aaab97..4d069c974 100644 --- a/modules/prokka/tests/main.nf.test.snap +++ b/modules/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-04-29T11:16:48.191157898", + "timestamp": "2026-07-28T17:05:06.405344361", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-04-29T11:17:22.119737635", + "timestamp": "2026-07-28T17:05:40.570755671", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-27T14:10:11.585993926", + "timestamp": "2026-07-28T17:06:26.671459009", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/prokka/tests/nextflow.config b/modules/prokka/tests/nextflow.config index a3ef0d7c6..ff2763d44 100644 --- a/modules/prokka/tests/nextflow.config +++ b/modules/prokka/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of PROKKA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,27 +11,9 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" // Under nf-test, projectDir is this tests/ directory bactopia_dir = "${projectDir}/../../.." - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/quast/tests/main.nf.test.snap b/modules/quast/tests/main.nf.test.snap index fd7455f79..317c69148 100644 --- a/modules/quast/tests/main.nf.test.snap +++ b/modules/quast/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-04-29T11:17:08.770591985", + "timestamp": "2026-07-28T17:05:23.753301259", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-04-29T11:16:46.344863097", + "timestamp": "2026-07-28T17:05:01.575708819", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-04-29T11:16:20.405215733", + "timestamp": "2026-07-28T17:04:36.267729238", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/quast/tests/nextflow.config b/modules/quast/tests/nextflow.config index 613929103..cab070af7 100644 --- a/modules/quast/tests/nextflow.config +++ b/modules/quast/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of QUAST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/rgi/heatmap/module.config b/modules/rgi/heatmap/module.config index ef292b45d..df6c71fb2 100644 --- a/modules/rgi/heatmap/module.config +++ b/modules/rgi/heatmap/module.config @@ -19,9 +19,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::rgi=6.0.5".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/rgi:6.0.5--pyh05cac1d_0" - ext.image = "https://depot.galaxyproject.org/singularity/rgi:6.0.5--pyh05cac1d_0" + ext.toolName = "bioconda::rgi=6.0.8".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/rgi:6.0.8--pyh05cac1d_0" + ext.image = "https://depot.galaxyproject.org/singularity/rgi:6.0.8--pyh05cac1d_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/rgi/heatmap/tests/main.nf.test.snap b/modules/rgi/heatmap/tests/main.nf.test.snap index 905e6605f..f401efa7f 100644 --- a/modules/rgi/heatmap/tests/main.nf.test.snap +++ b/modules/rgi/heatmap/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "run" }, [ - "versions.yml:md5,632aee3b4ff52c9313a58f423eeed956" + "versions.yml:md5,85fd687a901fef3c05e188fe49391c68" ] ], - "timestamp": "2026-04-29T11:16:27.891122241", + "timestamp": "2026-07-28T17:04:40.292532375", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/heatmap/tests/nextflow.config b/modules/rgi/heatmap/tests/nextflow.config index d70b3befe..17421413a 100644 --- a/modules/rgi/heatmap/tests/nextflow.config +++ b/modules/rgi/heatmap/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of RGI_HEATMAP nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // RGI heatmap parameters (referenced in module.config) rgi_frequency = false diff --git a/modules/rgi/main/main.nf b/modules/rgi/main/main.nf index dead66576..f5392f595 100644 --- a/modules/rgi/main/main.nf +++ b/modules/rgi/main/main.nf @@ -68,7 +68,7 @@ process RGI_MAIN { ${task.ext.args} \\ --clean \\ --data wgs \\ - --num_threads ${task.cpus} \\ + --threads ${task.cpus} \\ --output_file ${prefix} \\ --input_sequence ${fna} diff --git a/modules/rgi/main/module.config b/modules/rgi/main/module.config index 310d070c8..554d70add 100644 --- a/modules/rgi/main/module.config +++ b/modules/rgi/main/module.config @@ -3,7 +3,7 @@ params { rgi_category = "" rgi_cluster = "" rgi_display = "plain" - rgi_exclude_nudge = false + rgi_include_nudge = false rgi_frequency = false rgi_include_loose = false rgi_use_diamond = false @@ -21,13 +21,13 @@ process { ext.args = [ params.rgi_use_diamond ? "--alignment_tool DIAMOND" : "--alignment_tool BLAST", params.rgi_include_loose ? "--include_loose" : "", - params.rgi_exclude_nudge ? "--exclude_nudge" : "" + params.rgi_include_nudge ? "--include_nudge" : "" ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::rgi=6.0.5".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/rgi:6.0.5--pyh05cac1d_0" - ext.image = "https://depot.galaxyproject.org/singularity/rgi:6.0.5--pyh05cac1d_0" + ext.toolName = "bioconda::rgi=6.0.8".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/rgi:6.0.8--pyh05cac1d_0" + ext.image = "https://depot.galaxyproject.org/singularity/rgi:6.0.8--pyh05cac1d_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/rgi/main/schema.json b/modules/rgi/main/schema.json index ed7854372..094475622 100644 --- a/modules/rgi/main/schema.json +++ b/modules/rgi/main/schema.json @@ -25,10 +25,10 @@ "fa_icon": "fas fa-toggle-on", "hidden": true }, - "rgi_exclude_nudge": { + "rgi_include_nudge": { "type": "boolean", "default": false, - "description": "Exclude hits nudged from loose to strict hits", + "description": "Include hits nudged from loose to strict hits", "fa_icon": "fas fa-toggle-on", "hidden": true }, diff --git a/modules/rgi/main/tests/main.nf.test b/modules/rgi/main/tests/main.nf.test index 84ae4cf4e..5ff1c770e 100644 --- a/modules/rgi/main/tests/main.nf.test +++ b/modules/rgi/main/tests/main.nf.test @@ -65,4 +65,35 @@ nextflow_process { ) } } + + test("rgi - module - GCF_900478275 - include_nudge") { + when { + params { + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" + rgi_include_nudge = true + } + process { + """ + input[0] = Channel.of( + record( + meta: [name: "GCF_900478275"], + fna: file("${params.test_data_dir}/species/haemophilus_influenzae/compressed/GCF_900478275/main/assembler/GCF_900478275.fna.gz") + ) + ) + """ + } + } + + then { + def record = process.out[0][0] + assertAll( + { assert process.success }, + { assert snapshot( + record.meta, + record.tsv, + record.versions + ).match() } + ) + } + } } diff --git a/modules/rgi/main/tests/main.nf.test.snap b/modules/rgi/main/tests/main.nf.test.snap index 61dff38a6..5e4c9819a 100644 --- a/modules/rgi/main/tests/main.nf.test.snap +++ b/modules/rgi/main/tests/main.nf.test.snap @@ -9,12 +9,33 @@ "process_name": "rgi_main", "scope": "sample" }, - "GCF_900478275.tsv:md5,9d7754551163e020beed52a8bc14ce83", + "GCF_900478275.tsv:md5,9dd0afe6946da9c6608e775f954813a1", [ - "versions.yml:md5,238ddd7a4b55d8797a1d5bfc111ebbfd" + "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-04-29T11:17:22.355042061", + "timestamp": "2026-07-28T18:26:02.309171001", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "rgi - module - GCF_900478275 - include_nudge": { + "content": [ + { + "id": "GCF_900478275-RGI_MAIN", + "logs_dir": "GCF_900478275/tools/rgi_main//logs/", + "name": "GCF_900478275", + "output_dir": "GCF_900478275/tools/rgi_main/", + "process_name": "rgi_main", + "scope": "sample" + }, + "GCF_900478275.tsv:md5,9dd0afe6946da9c6608e775f954813a1", + [ + "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" + ] + ], + "timestamp": "2026-07-28T18:27:17.03098611", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -30,12 +51,12 @@ "process_name": "rgi_main", "scope": "sample" }, - "GCA_000027305.tsv:md5,4207abf2986a420c0fb15b33e77144a6", + "GCA_000027305.tsv:md5,9af9b3e370a908d6b86a21c2cecad254", [ - "versions.yml:md5,238ddd7a4b55d8797a1d5bfc111ebbfd" + "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-04-29T11:18:41.325231847", + "timestamp": "2026-07-28T18:26:38.946091259", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/main/tests/nextflow.config b/modules/rgi/main/tests/nextflow.config index 157f73837..45cc8dde0 100644 --- a/modules/rgi/main/tests/nextflow.config +++ b/modules/rgi/main/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of RGI_MAIN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/roary/tests/main.nf.test.snap b/modules/roary/tests/main.nf.test.snap index 25e67cba3..37718da98 100644 --- a/modules/roary/tests/main.nf.test.snap +++ b/modules/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,80c99c1b38b33ebcb7925eabba7ca2eb" ] ], - "timestamp": "2026-04-29T11:17:54.404327622", + "timestamp": "2026-07-28T17:06:06.835395759", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/roary/tests/nextflow.config b/modules/roary/tests/nextflow.config index be29306b1..b5ea61f7d 100644 --- a/modules/roary/tests/nextflow.config +++ b/modules/roary/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of ROARY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/sccmec/tests/main.nf.test.snap b/modules/sccmec/tests/main.nf.test.snap index 9a494cd0a..939020664 100644 --- a/modules/sccmec/tests/main.nf.test.snap +++ b/modules/sccmec/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" ] ], - "timestamp": "2026-04-29T11:16:25.913673101", + "timestamp": "2026-07-28T17:04:42.233854202", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" ] ], - "timestamp": "2026-04-29T11:16:45.324766261", + "timestamp": "2026-07-28T17:05:02.684305186", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sccmec/tests/nextflow.config b/modules/sccmec/tests/nextflow.config index 66595a4fc..331192f56 100644 --- a/modules/sccmec/tests/nextflow.config +++ b/modules/sccmec/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SCCMEC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/scoary/tests/main.nf.test.snap b/modules/scoary/tests/main.nf.test.snap index 04319727a..2a4340347 100644 --- a/modules/scoary/tests/main.nf.test.snap +++ b/modules/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,f8f8a2300f84de4e8184c9dd33579ccd" ] ], - "timestamp": "2026-04-29T11:16:20.893786706", + "timestamp": "2026-07-28T17:04:39.878685538", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/scoary/tests/nextflow.config b/modules/scoary/tests/nextflow.config index 7a3abcfce..e65e7b643 100644 --- a/modules/scoary/tests/nextflow.config +++ b/modules/scoary/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SCOARY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/seqsero2/tests/main.nf.test.snap b/modules/seqsero2/tests/main.nf.test.snap index ebea9c714..951b747c7 100644 --- a/modules/seqsero2/tests/main.nf.test.snap +++ b/modules/seqsero2/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-04-29T11:16:38.436546661", + "timestamp": "2026-07-28T17:04:56.44659963", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-04-29T11:16:24.056038097", + "timestamp": "2026-07-28T17:04:40.02602688", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seqsero2/tests/nextflow.config b/modules/seqsero2/tests/nextflow.config index 4db50f9d3..e81bf8a99 100644 --- a/modules/seqsero2/tests/nextflow.config +++ b/modules/seqsero2/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SEQSERO2 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/seroba/run/tests/main.nf.test.snap b/modules/seroba/run/tests/main.nf.test.snap index 90c0502ca..958e3ad60 100644 --- a/modules/seroba/run/tests/main.nf.test.snap +++ b/modules/seroba/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,e485bb335ccae3f5e5f24f35690633d3" ] ], - "timestamp": "2026-04-29T11:17:01.34899278", + "timestamp": "2026-07-28T17:05:10.585666494", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seroba/run/tests/nextflow.config b/modules/seroba/run/tests/nextflow.config index 1388b8558..6b1c8fcd3 100644 --- a/modules/seroba/run/tests/nextflow.config +++ b/modules/seroba/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SEROBA_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/shigapass/tests/main.nf.test.snap b/modules/shigapass/tests/main.nf.test.snap index 1308cac22..62010e8e9 100644 --- a/modules/shigapass/tests/main.nf.test.snap +++ b/modules/shigapass/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-04-29T11:16:40.848025485", + "timestamp": "2026-07-28T17:04:53.170596966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-04-29T11:17:08.640530652", + "timestamp": "2026-07-28T17:05:20.818727304", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigapass/tests/nextflow.config b/modules/shigapass/tests/nextflow.config index e1b288aa1..d1730ad32 100644 --- a/modules/shigapass/tests/nextflow.config +++ b/modules/shigapass/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SHIGAPASS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/shigatyper/tests/main.nf.test.snap b/modules/shigatyper/tests/main.nf.test.snap index 7fed17c83..093064a7b 100644 --- a/modules/shigatyper/tests/main.nf.test.snap +++ b/modules/shigatyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,5546505c7719718340a0cd98ece587d8" ] ], - "timestamp": "2026-04-29T11:16:34.193573039", + "timestamp": "2026-07-28T17:04:47.911451164", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigatyper/tests/nextflow.config b/modules/shigatyper/tests/nextflow.config index 6503f2cf6..a5f6991f7 100644 --- a/modules/shigatyper/tests/nextflow.config +++ b/modules/shigatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SHIGATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/shigeifinder/tests/main.nf.test.snap b/modules/shigeifinder/tests/main.nf.test.snap index 79781bf30..06b0e55de 100644 --- a/modules/shigeifinder/tests/main.nf.test.snap +++ b/modules/shigeifinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-04-29T11:16:45.805440428", + "timestamp": "2026-07-28T17:04:57.786169176", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-04-29T11:16:31.145144861", + "timestamp": "2026-07-28T17:04:42.412647302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigeifinder/tests/nextflow.config b/modules/shigeifinder/tests/nextflow.config index afe392eee..b43094903 100644 --- a/modules/shigeifinder/tests/nextflow.config +++ b/modules/shigeifinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SHIGEIFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/sistr/tests/main.nf.test.snap b/modules/sistr/tests/main.nf.test.snap index 4ea1e6c7f..1aecda476 100644 --- a/modules/sistr/tests/main.nf.test.snap +++ b/modules/sistr/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-04-29T11:17:03.830490041", + "timestamp": "2026-07-28T17:05:16.274198697", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-04-29T11:17:46.465617002", + "timestamp": "2026-07-28T17:05:59.227307511", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sistr/tests/nextflow.config b/modules/sistr/tests/nextflow.config index 6ccd4ab70..3ae4c9503 100644 --- a/modules/sistr/tests/nextflow.config +++ b/modules/sistr/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SISTR nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/snippy/core/tests/main.nf.test.snap b/modules/snippy/core/tests/main.nf.test.snap index 39efb184a..d20b48d20 100644 --- a/modules/snippy/core/tests/main.nf.test.snap +++ b/modules/snippy/core/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,af05caa4daa181fbe9d7bf82d3383d93" ] ], - "timestamp": "2026-04-29T11:16:41.365495425", + "timestamp": "2026-07-28T17:04:53.721386457", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/core/tests/nextflow.config b/modules/snippy/core/tests/nextflow.config index 3dc05b65b..26bc1b8b0 100644 --- a/modules/snippy/core/tests/nextflow.config +++ b/modules/snippy/core/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SNIPPY_CORE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,27 +11,9 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true run_name = "snippy" - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - // Module-specific defaults skip_compression = false } diff --git a/modules/snippy/run/tests/main.nf.test.snap b/modules/snippy/run/tests/main.nf.test.snap index bdfcd9fe6..b47d6a618 100644 --- a/modules/snippy/run/tests/main.nf.test.snap +++ b/modules/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-04-29T11:17:53.084972353", + "timestamp": "2026-07-28T17:06:03.703638294", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-04-29T11:17:11.210462885", + "timestamp": "2026-07-28T17:05:24.72141497", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/run/tests/nextflow.config b/modules/snippy/run/tests/nextflow.config index 9090849dd..1fba30717 100644 --- a/modules/snippy/run/tests/nextflow.config +++ b/modules/snippy/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SNIPPY_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,27 +11,9 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true run_name = "snippy" - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - // Module-specific defaults skip_compression = false } diff --git a/modules/snpdists/tests/main.nf.test.snap b/modules/snpdists/tests/main.nf.test.snap index a90886d43..8603b959c 100644 --- a/modules/snpdists/tests/main.nf.test.snap +++ b/modules/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,944b6ecf9bf11c38b608ae08b36d5e2d" ] ], - "timestamp": "2026-04-29T11:16:44.89235401", + "timestamp": "2026-07-28T17:04:56.460770293", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snpdists/tests/nextflow.config b/modules/snpdists/tests/nextflow.config index 0d9d0caca..b5ee788a7 100644 --- a/modules/snpdists/tests/nextflow.config +++ b/modules/snpdists/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SNPDISTS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/spatyper/tests/main.nf.test.snap b/modules/spatyper/tests/main.nf.test.snap index 7e1fc41c0..4f5cc54be 100644 --- a/modules/spatyper/tests/main.nf.test.snap +++ b/modules/spatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-04-29T11:17:14.808148328", + "timestamp": "2026-07-28T17:05:27.906825448", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-04-29T11:16:54.28753732", + "timestamp": "2026-07-28T17:05:07.974904548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/spatyper/tests/nextflow.config b/modules/spatyper/tests/nextflow.config index 5474aeeec..ea51695d7 100644 --- a/modules/spatyper/tests/nextflow.config +++ b/modules/spatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SPATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap index 2322ac9d0..441fbcf6c 100644 --- a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap +++ b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-04-29T11:18:53.83883245", + "timestamp": "2026-07-28T17:07:04.704034393", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-04-29T11:18:00.849936857", + "timestamp": "2026-07-28T17:06:15.637730118", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/srahumanscrubber/scrub/tests/nextflow.config b/modules/srahumanscrubber/scrub/tests/nextflow.config index cb859d08a..45c27ca5d 100644 --- a/modules/srahumanscrubber/scrub/tests/nextflow.config +++ b/modules/srahumanscrubber/scrub/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SRAHUMANSCRUBBER_SCRUB nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/ssuissero/tests/main.nf.test.snap b/modules/ssuissero/tests/main.nf.test.snap index 12d3d22ce..3f6a5a4b9 100644 --- a/modules/ssuissero/tests/main.nf.test.snap +++ b/modules/ssuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-04-29T11:16:48.923659704", + "timestamp": "2026-07-28T17:05:03.055657376", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-04-29T11:17:04.393761797", + "timestamp": "2026-07-28T17:05:16.698142582", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ssuissero/tests/nextflow.config b/modules/ssuissero/tests/nextflow.config index b31f6d479..2309866e1 100644 --- a/modules/ssuissero/tests/nextflow.config +++ b/modules/ssuissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SSUISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/staphopiasccmec/tests/main.nf.test.snap b/modules/staphopiasccmec/tests/main.nf.test.snap index 338d96c60..5b73071c8 100644 --- a/modules/staphopiasccmec/tests/main.nf.test.snap +++ b/modules/staphopiasccmec/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-04-29T11:16:51.320618453", + "timestamp": "2026-07-28T17:05:04.955792698", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-04-29T11:17:06.354030176", + "timestamp": "2026-07-28T17:05:18.97449695", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphopiasccmec/tests/nextflow.config b/modules/staphopiasccmec/tests/nextflow.config index c56f134cd..3cfb5710b 100644 --- a/modules/staphopiasccmec/tests/nextflow.config +++ b/modules/staphopiasccmec/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of STAPHOPIASCCMEC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/staphscan/module.config b/modules/staphscan/module.config index 9d901351e..a15f3d49e 100644 --- a/modules/staphscan/module.config +++ b/modules/staphscan/module.config @@ -17,9 +17,9 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::staphscan=0.3.1".replace("=", "-").replace(":", "-").replace(" ", "-") - ext.docker = "biocontainers/staphscan:0.3.1--pyhdfd78af_0" - ext.image = "https://depot.galaxyproject.org/singularity/staphscan:0.3.1--pyhdfd78af_0" + ext.toolName = "bioconda::staphscan=0.4.1".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.docker = "biocontainers/staphscan:0.4.1--pyhdfd78af_0" + ext.image = "https://depot.galaxyproject.org/singularity/staphscan:0.4.1--pyhdfd78af_0" ext.condaDir = "${params.condadir}" } } diff --git a/modules/staphscan/tests/main.nf.test.snap b/modules/staphscan/tests/main.nf.test.snap index 65503ccd7..cd8c4b23b 100644 --- a/modules/staphscan/tests/main.nf.test.snap +++ b/modules/staphscan/tests/main.nf.test.snap @@ -9,12 +9,12 @@ "process_name": "staphscan", "scope": "sample" }, - "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + "GCF_000017085.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e", [ - "versions.yml:md5,466b4f78a712b55acb9520437caf3fea" + "versions.yml:md5,251f3e6b35be5f660d5fc8bc8456bde6" ] ], - "timestamp": "2026-05-05T12:02:27.973597404", + "timestamp": "2026-07-28T17:05:19.361127758", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphscan/tests/nextflow.config b/modules/staphscan/tests/nextflow.config index 91e332961..df04b2b63 100644 --- a/modules/staphscan/tests/nextflow.config +++ b/modules/staphscan/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of STAPHSCAN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/stecfinder/tests/main.nf.test.snap b/modules/stecfinder/tests/main.nf.test.snap index a09453759..da2337601 100644 --- a/modules/stecfinder/tests/main.nf.test.snap +++ b/modules/stecfinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-04-29T11:17:24.705508456", + "timestamp": "2026-07-28T17:05:37.98973119", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-04-29T11:17:09.146129519", + "timestamp": "2026-07-28T17:05:22.061014948", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-04-29T11:16:54.388692462", + "timestamp": "2026-07-28T17:05:06.285732415", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stecfinder/tests/nextflow.config b/modules/stecfinder/tests/nextflow.config index ad70d6b3f..d63587108 100644 --- a/modules/stecfinder/tests/nextflow.config +++ b/modules/stecfinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of STECFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/stxtyper/tests/main.nf.test.snap b/modules/stxtyper/tests/main.nf.test.snap index cbb4803c2..4083d438f 100644 --- a/modules/stxtyper/tests/main.nf.test.snap +++ b/modules/stxtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9ebd9c1f28e4ce3da541f707abeaa52" ] ], - "timestamp": "2026-05-21T13:54:27.24411333", + "timestamp": "2026-07-28T17:05:08.497632821", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stxtyper/tests/nextflow.config b/modules/stxtyper/tests/nextflow.config index ca3810ec1..aff4b77b5 100644 --- a/modules/stxtyper/tests/nextflow.config +++ b/modules/stxtyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of STXTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/sylph/profile/tests/main.nf.test.snap b/modules/sylph/profile/tests/main.nf.test.snap index cddad7329..713b13634 100644 --- a/modules/sylph/profile/tests/main.nf.test.snap +++ b/modules/sylph/profile/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-04-29T11:19:04.101178065", + "timestamp": "2026-07-28T17:07:11.970567672", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-04-29T11:17:52.980299022", + "timestamp": "2026-07-28T17:06:02.478428995", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sylph/profile/tests/nextflow.config b/modules/sylph/profile/tests/nextflow.config index 2f52ae289..5fc47b72f 100644 --- a/modules/sylph/profile/tests/nextflow.config +++ b/modules/sylph/profile/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of SYLPH_PROFILE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,10 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 12 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/tbprofiler/collate/tests/main.nf.test.snap b/modules/tbprofiler/collate/tests/main.nf.test.snap index b48ccf877..d27931aba 100644 --- a/modules/tbprofiler/collate/tests/main.nf.test.snap +++ b/modules/tbprofiler/collate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,3c3d5fbb783c5cb96c154683bf56699a" ] ], - "timestamp": "2026-04-29T11:16:59.178764406", + "timestamp": "2026-07-28T17:05:13.493314477", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/collate/tests/nextflow.config b/modules/tbprofiler/collate/tests/nextflow.config index 44b8d4888..9b4c1ed10 100644 --- a/modules/tbprofiler/collate/tests/nextflow.config +++ b/modules/tbprofiler/collate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of TBPROFILER_COLLATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/tbprofiler/profile/tests/main.nf.test.snap b/modules/tbprofiler/profile/tests/main.nf.test.snap index fbaabbd27..e4a700806 100644 --- a/modules/tbprofiler/profile/tests/main.nf.test.snap +++ b/modules/tbprofiler/profile/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-04-29T11:17:48.441284413", + "timestamp": "2026-07-28T17:06:05.654435437", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-04-29T11:18:45.03550605", + "timestamp": "2026-07-28T17:07:00.071655149", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-04-29T11:19:51.614736697", + "timestamp": "2026-07-28T17:08:04.874956479", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/profile/tests/nextflow.config b/modules/tbprofiler/profile/tests/nextflow.config index 83b690a93..e19bb6e2b 100644 --- a/modules/tbprofiler/profile/tests/nextflow.config +++ b/modules/tbprofiler/profile/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of TBPROFILER_PROFILE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/modules/traitar/run/tests/main.nf.test.snap b/modules/traitar/run/tests/main.nf.test.snap index dba1061f2..092f218f5 100644 --- a/modules/traitar/run/tests/main.nf.test.snap +++ b/modules/traitar/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-05-06T08:19:10.186774203", + "timestamp": "2026-07-28T17:11:13.940393717", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-05-06T08:22:03.435009482", + "timestamp": "2026-07-28T17:16:29.759672024", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/traitar/run/tests/nextflow.config b/modules/traitar/run/tests/nextflow.config index 35a2ab164..1c3597475 100644 --- a/modules/traitar/run/tests/nextflow.config +++ b/modules/traitar/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for module-level testing of TRAITAR_RUN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } includeConfig "../module.config" diff --git a/nextflow.config b/nextflow.config index 20065c0e1..c46bb15d3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/nextflow_schema.json b/nextflow_schema.json index 8a3e48c6b..870ff8086 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -472,12 +472,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-toggle-on", - "hidden": true } } }, diff --git a/subworkflows/abricate/tests/main.nf.test.snap b/subworkflows/abricate/tests/main.nf.test.snap index 8bcd7df8d..af3e7b572 100644 --- a/subworkflows/abricate/tests/main.nf.test.snap +++ b/subworkflows/abricate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-04-29T11:17:01.332607084", + "timestamp": "2026-07-28T17:05:24.089706956", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abricate/tests/nextflow.config b/subworkflows/abricate/tests/nextflow.config index 829218003..fdebc9d67 100644 --- a/subworkflows/abricate/tests/nextflow.config +++ b/subworkflows/abricate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ABRICATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Mass screening of contigs for antimicrobial and virulence genes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for both processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/abricate/summary/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/abritamr/tests/main.nf.test.snap b/subworkflows/abritamr/tests/main.nf.test.snap index c8e2a1826..d05b4ace9 100644 --- a/subworkflows/abritamr/tests/main.nf.test.snap +++ b/subworkflows/abritamr/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "sample" }, [ - "versions.yml:md5,aa30fa16abc1d1a9baefd6defd920a32" + "versions.yml:md5,ef1b96216865ffadde25334b59f3361c" ], { "id": "abritamr-ABRITAMR:CSVTK_CONCAT", @@ -24,7 +24,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-04-29T11:21:12.012980197", + "timestamp": "2026-07-28T17:09:35.722894995", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abritamr/tests/nextflow.config b/subworkflows/abritamr/tests/nextflow.config index 7681f58b4..1a92ac855 100644 --- a/subworkflows/abritamr/tests/nextflow.config +++ b/subworkflows/abritamr/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ABRITAMR nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "AMR gene detection using AMRFinderPlus" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/agrvate/tests/main.nf.test.snap b/subworkflows/agrvate/tests/main.nf.test.snap index 9d6a12271..060975856 100644 --- a/subworkflows/agrvate/tests/main.nf.test.snap +++ b/subworkflows/agrvate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-04-29T11:17:03.806343444", + "timestamp": "2026-07-28T17:05:29.324054494", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/agrvate/tests/nextflow.config b/subworkflows/agrvate/tests/nextflow.config index 1ebdea255..db4afbe2f 100644 --- a/subworkflows/agrvate/tests/nextflow.config +++ b/subworkflows/agrvate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of AGRVATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Rapid identification of agr locus type and agr operon variants" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/amrfinderplus/tests/main.nf.test.snap b/subworkflows/amrfinderplus/tests/main.nf.test.snap index c0e408756..0e28895a8 100644 --- a/subworkflows/amrfinderplus/tests/main.nf.test.snap +++ b/subworkflows/amrfinderplus/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-04-29T11:17:16.329849997", + "timestamp": "2026-07-28T17:05:38.084290058", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/amrfinderplus/tests/nextflow.config b/subworkflows/amrfinderplus/tests/nextflow.config index 5042cf02a..1820cd945 100644 --- a/subworkflows/amrfinderplus/tests/nextflow.config +++ b/subworkflows/amrfinderplus/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of AMRFINDERPLUS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Identify AMR genes and mutations" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ariba/tests/main.nf.test.snap b/subworkflows/ariba/tests/main.nf.test.snap index 4fd59133d..0f5834aa1 100644 --- a/subworkflows/ariba/tests/main.nf.test.snap +++ b/subworkflows/ariba/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6" ] ], - "timestamp": "2026-04-29T11:25:44.116364415", + "timestamp": "2026-07-28T17:12:37.41821209", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ariba/tests/nextflow.config b/subworkflows/ariba/tests/nextflow.config index 5e44ac983..57e6d83eb 100644 --- a/subworkflows/ariba/tests/nextflow.config +++ b/subworkflows/ariba/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ARIBA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Antimicrobial resistance gene identification by assembly" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/bactopia/assembler/tests/nextflow.config b/subworkflows/bactopia/assembler/tests/nextflow.config index 4d89e7ac3..5a5bbb4f7 100644 --- a/subworkflows/bactopia/assembler/tests/nextflow.config +++ b/subworkflows/bactopia/assembler/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ASSEMBLER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,26 +11,11 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB max_cpus = 12 - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" - // Module-specific defaults contig_namefmt = "contig%05d" dragonflye_assembler = "flye" @@ -65,7 +51,3 @@ includeConfig "../../../../modules/bactopia/assembler/module.config" includeConfig "../../../../modules/csvtk/concat/module.config" includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" - -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/bactopia/datasets/tests/nextflow.config b/subworkflows/bactopia/datasets/tests/nextflow.config index 2168f2b7d..b3cad7d4d 100644 --- a/subworkflows/bactopia/datasets/tests/nextflow.config +++ b/subworkflows/bactopia/datasets/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of DATASETS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,30 +11,12 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults datasets_cache = "${params.bactopia_cache}/datasets" amrfinderplus_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/amrfinderplus.tar.gz" - mlst_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/mlst.tar.gz" + mlst_url = "https://datasets.bactopia.com/datasets/mlst.tar.gz" mash_url = "https://datasets.bactopia.com/datasets/mash-refseq88.k21.msh.xz" sourmash_url = "https://datasets.bactopia.com/datasets/gtdb-rs207.genomic-reps.dna.k31.lca.json.gz" } diff --git a/subworkflows/bactopia/qc/tests/nextflow.config b/subworkflows/bactopia/qc/tests/nextflow.config index a89cb2fa5..608dfe256 100644 --- a/subworkflows/bactopia/qc/tests/nextflow.config +++ b/subworkflows/bactopia/qc/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of QC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -10,25 +11,7 @@ params { ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - - // Max Job Request Parameters - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - - // Nextflow Profile Parameters - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults adapter_k = 23 @@ -71,7 +54,3 @@ params { includeConfig "../../../../modules/bactopia/qc/module.config" includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" - -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap index fbe36d796..65f0941b3 100644 --- a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap +++ b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e46de3078794860a978e2dd0b390c27c" ] ], - "timestamp": "2026-04-29T11:18:38.450245363", + "timestamp": "2026-07-28T17:06:50.814548918", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bactopia/sketcher/tests/nextflow.config b/subworkflows/bactopia/sketcher/tests/nextflow.config index 882fb3df0..54d2c1894 100644 --- a/subworkflows/bactopia/sketcher/tests/nextflow.config +++ b/subworkflows/bactopia/sketcher/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SKETCHER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Sketch sequences for rapid comparisons" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../../modules/bactopia/sketcher/module.config" // Base config (container resolution + resource labels) includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/bakta/tests/main.nf.test.snap b/subworkflows/bakta/tests/main.nf.test.snap index bb807384e..c1d34bef4 100644 --- a/subworkflows/bakta/tests/main.nf.test.snap +++ b/subworkflows/bakta/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-04-29T11:21:33.858162803", + "timestamp": "2026-07-28T17:09:33.812878779", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bakta/tests/nextflow.config b/subworkflows/bakta/tests/nextflow.config index 40001ff16..5f12005da 100644 --- a/subworkflows/bakta/tests/nextflow.config +++ b/subworkflows/bakta/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BAKTA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Rapid annotation of bacterial genomes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/bakta/run/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/blastn/tests/main.nf.test.snap b/subworkflows/blastn/tests/main.nf.test.snap index d48a73c72..2a55326c6 100644 --- a/subworkflows/blastn/tests/main.nf.test.snap +++ b/subworkflows/blastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-04-29T11:17:32.153667352", + "timestamp": "2026-07-28T17:05:44.851740724", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastn/tests/nextflow.config b/subworkflows/blastn/tests/nextflow.config index b2347317e..172f1963a 100644 --- a/subworkflows/blastn/tests/nextflow.config +++ b/subworkflows/blastn/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BLASTN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "BLAST blastn search" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/blastp/tests/main.nf.test.snap b/subworkflows/blastp/tests/main.nf.test.snap index b0571c9c3..87acd319f 100644 --- a/subworkflows/blastp/tests/main.nf.test.snap +++ b/subworkflows/blastp/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-04-29T11:17:32.89753947", + "timestamp": "2026-07-28T17:05:45.638516837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastp/tests/nextflow.config b/subworkflows/blastp/tests/nextflow.config index 72c82e788..9edf79625 100644 --- a/subworkflows/blastp/tests/nextflow.config +++ b/subworkflows/blastp/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BLASTP nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "BLAST blastp search" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/blastx/tests/main.nf.test.snap b/subworkflows/blastx/tests/main.nf.test.snap index 83d29f22e..c3bd8b7c7 100644 --- a/subworkflows/blastx/tests/main.nf.test.snap +++ b/subworkflows/blastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-04-29T11:17:32.589699334", + "timestamp": "2026-07-28T17:05:48.712350516", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastx/tests/nextflow.config b/subworkflows/blastx/tests/nextflow.config index 107e76f54..09d62505e 100644 --- a/subworkflows/blastx/tests/nextflow.config +++ b/subworkflows/blastx/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BLASTX nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "BLAST blastx search" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/bracken/tests/nextflow.config b/subworkflows/bracken/tests/nextflow.config index 1fc6e966f..8e2f8357b 100644 --- a/subworkflows/bracken/tests/nextflow.config +++ b/subworkflows/bracken/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BRACKEN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Bayesian reestimation of abundance with KrakEN" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/btyper3/tests/main.nf.test.snap b/subworkflows/btyper3/tests/main.nf.test.snap index 6d5b7a6c3..283728ec8 100644 --- a/subworkflows/btyper3/tests/main.nf.test.snap +++ b/subworkflows/btyper3/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-04-29T11:19:27.531463029", + "timestamp": "2026-07-28T17:07:34.749578586", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/btyper3/tests/nextflow.config b/subworkflows/btyper3/tests/nextflow.config index c4ce1f7a8..151b5b2dc 100644 --- a/subworkflows/btyper3/tests/nextflow.config +++ b/subworkflows/btyper3/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BTYPER3 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Virulence typing of Bacillus cereus group isolates" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/busco/tests/main.nf.test.snap b/subworkflows/busco/tests/main.nf.test.snap index fefc16b56..208e9463c 100644 --- a/subworkflows/busco/tests/main.nf.test.snap +++ b/subworkflows/busco/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "SRR2838702-summary.txt:md5,d1cbbfb9ab7dee0204bfa26f3b982620", [ - "versions.yml:md5,84a39022a8e62bb5b3eb9c860e79d49f" + "versions.yml:md5,bfe8448c1dd05af49ff6b67f38a9db01" ], { "id": "busco-bacteria_odb10-BUSCO:CSVTK_CONCAT", @@ -25,7 +25,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-04-29T11:18:05.722136134", + "timestamp": "2026-07-28T17:06:16.389757249", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/busco/tests/nextflow.config b/subworkflows/busco/tests/nextflow.config index ec93f2248..667987685 100644 --- a/subworkflows/busco/tests/nextflow.config +++ b/subworkflows/busco/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of BUSCO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Assembly quality assessment using BUSCO" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/checkm/tests/main.nf.test.snap b/subworkflows/checkm/tests/main.nf.test.snap index 4fab1c018..916abbaf3 100644 --- a/subworkflows/checkm/tests/main.nf.test.snap +++ b/subworkflows/checkm/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-04-29T11:19:47.690709387", + "timestamp": "2026-07-28T17:08:01.285199969", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm/tests/nextflow.config b/subworkflows/checkm/tests/nextflow.config index b29827030..a725c3858 100644 --- a/subworkflows/checkm/tests/nextflow.config +++ b/subworkflows/checkm/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of CHECKM nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Assess the quality of microbial genomes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/checkm2/tests/main.nf.test.snap b/subworkflows/checkm2/tests/main.nf.test.snap index dfb0c3731..5fb769251 100644 --- a/subworkflows/checkm2/tests/main.nf.test.snap +++ b/subworkflows/checkm2/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-04-29T11:22:31.986367958", + "timestamp": "2026-07-28T17:10:52.675813409", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm2/tests/nextflow.config b/subworkflows/checkm2/tests/nextflow.config index 1b025f6fe..50865cc51 100644 --- a/subworkflows/checkm2/tests/nextflow.config +++ b/subworkflows/checkm2/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of CHECKM2 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Rapid quality assessment of metagenome-assembled genomes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/clermontyping/tests/main.nf.test.snap b/subworkflows/clermontyping/tests/main.nf.test.snap index e55ed7a70..0649874c0 100644 --- a/subworkflows/clermontyping/tests/main.nf.test.snap +++ b/subworkflows/clermontyping/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-04-29T11:18:11.723431368", + "timestamp": "2026-07-28T17:06:19.527120521", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clermontyping/tests/nextflow.config b/subworkflows/clermontyping/tests/nextflow.config index faa6a2663..9a5cf0771 100644 --- a/subworkflows/clermontyping/tests/nextflow.config +++ b/subworkflows/clermontyping/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of CLERMONTYPING nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico Clermont typing of Escherichia coli" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/clonalframeml/tests/main.nf.test.snap b/subworkflows/clonalframeml/tests/main.nf.test.snap index 30db0a4d4..3a9733ef1 100644 --- a/subworkflows/clonalframeml/tests/main.nf.test.snap +++ b/subworkflows/clonalframeml/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "scope": "run" }, [ - "versions.yml:md5,2998af40c25f65e228af5938ff93448e" + "versions.yml:md5,a8001abd80c493ec7ae6d20498bcd5bf" ], { "id": "core-genome.masked.distance-snpdists", @@ -40,7 +40,7 @@ "versions.yml:md5,77f64a20eeab9152a61953ec5203b926" ] ], - "timestamp": "2026-04-29T11:19:01.237617004", + "timestamp": "2026-07-28T17:07:09.542810063", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clonalframeml/tests/nextflow.config b/subworkflows/clonalframeml/tests/nextflow.config index 1f021ec7d..57c15b588 100644 --- a/subworkflows/clonalframeml/tests/nextflow.config +++ b/subworkflows/clonalframeml/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of CLONALFRAMEML nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Recombination detection in bacterial genomes" ext = "aln" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/snpdists/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/deacon/tests/main.nf.test.snap b/subworkflows/deacon/tests/main.nf.test.snap index 20a945eaf..b3c366c35 100644 --- a/subworkflows/deacon/tests/main.nf.test.snap +++ b/subworkflows/deacon/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,9d3e1c1b5110e0048698861366ed5151" ] ], - "timestamp": "2026-05-06T14:31:09.736499752", + "timestamp": "2026-07-28T17:06:18.389528469", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/deacon/tests/nextflow.config b/subworkflows/deacon/tests/nextflow.config index 6c503aa7c..b01461736 100644 --- a/subworkflows/deacon/tests/nextflow.config +++ b/subworkflows/deacon/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of DEACON nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Remove host reads from sequencing data" ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for ALL processes used by this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/deacon/filter/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/defensefinder/tests/main.nf.test.snap b/subworkflows/defensefinder/tests/main.nf.test.snap index ffcdddfe2..5cfd2b865 100644 --- a/subworkflows/defensefinder/tests/main.nf.test.snap +++ b/subworkflows/defensefinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,cac1e24b64c152890e712ac2077fc111" ] ], - "timestamp": "2026-04-29T11:18:49.743429096", + "timestamp": "2026-07-28T17:06:58.344177395", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/defensefinder/tests/nextflow.config b/subworkflows/defensefinder/tests/nextflow.config index c6ed1717c..9c7177fb1 100644 --- a/subworkflows/defensefinder/tests/nextflow.config +++ b/subworkflows/defensefinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of DEFENSEFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Systematic search of defense systems in bacterial genomes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ectyper/tests/main.nf.test.snap b/subworkflows/ectyper/tests/main.nf.test.snap index e25ecb430..c14840981 100644 --- a/subworkflows/ectyper/tests/main.nf.test.snap +++ b/subworkflows/ectyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-04-29T11:18:18.668546291", + "timestamp": "2026-07-28T17:06:31.999569833", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ectyper/tests/nextflow.config b/subworkflows/ectyper/tests/nextflow.config index 6c2cedd63..5e1faa243 100644 --- a/subworkflows/ectyper/tests/nextflow.config +++ b/subworkflows/ectyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ECTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico serotyping of E. coli" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/eggnog/tests/main.nf.test.snap b/subworkflows/eggnog/tests/main.nf.test.snap index 39861bf5d..7ba729caa 100644 --- a/subworkflows/eggnog/tests/main.nf.test.snap +++ b/subworkflows/eggnog/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "sample" }, [ - "versions.yml:md5,1b179e895ab51b7321ae747976b92b31" + "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" ] ], - "timestamp": "2026-04-29T11:32:14.279719669", + "timestamp": "2026-07-28T17:20:20.187785155", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/eggnog/tests/nextflow.config b/subworkflows/eggnog/tests/nextflow.config index 7dc7f4bce..dc21f606b 100644 --- a/subworkflows/eggnog/tests/nextflow.config +++ b/subworkflows/eggnog/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of EGGNOG nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Functional annotation of proteins" ext = "faa" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/eggnog/mapper/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/emmtyper/tests/main.nf.test.snap b/subworkflows/emmtyper/tests/main.nf.test.snap index 7d6297552..f391c7286 100644 --- a/subworkflows/emmtyper/tests/main.nf.test.snap +++ b/subworkflows/emmtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-04-29T11:17:58.904730441", + "timestamp": "2026-07-28T17:06:14.717092187", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/emmtyper/tests/nextflow.config b/subworkflows/emmtyper/tests/nextflow.config index b67bb3859..801a493b2 100644 --- a/subworkflows/emmtyper/tests/nextflow.config +++ b/subworkflows/emmtyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of EMMTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "emm typing of Streptococcus pyogenes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/fastani/tests/main.nf.test.snap b/subworkflows/fastani/tests/main.nf.test.snap index 2acf006dd..526856891 100644 --- a/subworkflows/fastani/tests/main.nf.test.snap +++ b/subworkflows/fastani/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-04-29T11:18:02.732052682", + "timestamp": "2026-07-28T17:06:15.47249014", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/fastani/tests/nextflow.config b/subworkflows/fastani/tests/nextflow.config index d7ebb8a78..2d2f7a5b5 100644 --- a/subworkflows/fastani/tests/nextflow.config +++ b/subworkflows/fastani/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of FASTANI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Fast whole-genome similarity estimation" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/gamma/tests/main.nf.test.snap b/subworkflows/gamma/tests/main.nf.test.snap index ca7a9853f..945370a6c 100644 --- a/subworkflows/gamma/tests/main.nf.test.snap +++ b/subworkflows/gamma/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-04-29T11:18:06.233770567", + "timestamp": "2026-07-28T17:06:16.30177237", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gamma/tests/nextflow.config b/subworkflows/gamma/tests/nextflow.config index 6969b68d1..2bf7bcbb7 100644 --- a/subworkflows/gamma/tests/nextflow.config +++ b/subworkflows/gamma/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GAMMA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Gene Allele Mutation Microbial Assessment" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/genomedl/tests/main.nf.test.snap b/subworkflows/genomedl/tests/main.nf.test.snap index 107d81119..40aecc613 100644 --- a/subworkflows/genomedl/tests/main.nf.test.snap +++ b/subworkflows/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-27T10:39:14.382642688", + "timestamp": "2026-07-28T17:06:36.276146878", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-27T10:39:22.848479262", + "timestamp": "2026-07-28T17:06:53.898888401", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-27T10:39:06.172839858", + "timestamp": "2026-07-28T17:06:19.392094773", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genomedl/tests/nextflow.config b/subworkflows/genomedl/tests/nextflow.config index 62f503f48..77789e7f3 100644 --- a/subworkflows/genomedl/tests/nextflow.config +++ b/subworkflows/genomedl/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GENOMEDL nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Download genome assemblies from NCBI Datasets" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/genomedl/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/genotyphi/tests/main.nf.test.snap b/subworkflows/genotyphi/tests/main.nf.test.snap index 7331bd078..b655f0f77 100644 --- a/subworkflows/genotyphi/tests/main.nf.test.snap +++ b/subworkflows/genotyphi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-04-29T11:18:18.066146142", + "timestamp": "2026-07-28T17:06:31.069260965", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genotyphi/tests/nextflow.config b/subworkflows/genotyphi/tests/nextflow.config index 1052e746f..c4dd6070c 100644 --- a/subworkflows/genotyphi/tests/nextflow.config +++ b/subworkflows/genotyphi/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GENOTYPHI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Genotyping of Salmonella Typhi" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/gigatyper/tests/main.nf.test.snap b/subworkflows/gigatyper/tests/main.nf.test.snap index a55a9cfd3..97e52b1e2 100644 --- a/subworkflows/gigatyper/tests/main.nf.test.snap +++ b/subworkflows/gigatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-04-29T11:18:25.429358789", + "timestamp": "2026-07-28T17:06:35.919557255", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gigatyper/tests/nextflow.config b/subworkflows/gigatyper/tests/nextflow.config index dfa06e727..28228fc18 100644 --- a/subworkflows/gigatyper/tests/nextflow.config +++ b/subworkflows/gigatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GIGATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Run all available MLST schemes for a species against an assembly" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/gtdb/tests/main.nf.test.snap b/subworkflows/gtdb/tests/main.nf.test.snap index fab16dd53..6b352c031 100644 --- a/subworkflows/gtdb/tests/main.nf.test.snap +++ b/subworkflows/gtdb/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "sample" }, [ - "versions.yml:md5,738ac1f744a77df263f3b25b97a2748d" + "versions.yml:md5,07e1a7fe67e8f4acb512d2f15e50f6c3" ], { "id": "gtdb-GTDB:CSVTK_CONCAT", @@ -24,7 +24,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-04-29T11:23:21.173815412", + "timestamp": "2026-07-28T17:11:32.840424346", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gtdb/tests/nextflow.config b/subworkflows/gtdb/tests/nextflow.config index 2d309645d..19a778a33 100644 --- a/subworkflows/gtdb/tests/nextflow.config +++ b/subworkflows/gtdb/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GTDB nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "GTDB-Tk classification of bacterial genomes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/gubbins/tests/main.nf.test.snap b/subworkflows/gubbins/tests/main.nf.test.snap index 098d18076..5a76fd542 100644 --- a/subworkflows/gubbins/tests/main.nf.test.snap +++ b/subworkflows/gubbins/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,a8d93e0d6a006b32c088567301fe66c4" ] ], - "timestamp": "2026-04-29T11:18:39.624854003", + "timestamp": "2026-07-28T17:06:49.502506719", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gubbins/tests/nextflow.config b/subworkflows/gubbins/tests/nextflow.config index fa5f53203..e1f0b5796 100644 --- a/subworkflows/gubbins/tests/nextflow.config +++ b/subworkflows/gubbins/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of GUBBINS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Recombination detection in bacteria" ext = "aln" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/snpdists/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/hicap/tests/main.nf.test.snap b/subworkflows/hicap/tests/main.nf.test.snap index ac7c7a0f6..8aa20ff02 100644 --- a/subworkflows/hicap/tests/main.nf.test.snap +++ b/subworkflows/hicap/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-04-29T11:18:43.986977664", + "timestamp": "2026-07-28T17:06:54.161586632", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hicap/tests/nextflow.config b/subworkflows/hicap/tests/nextflow.config index d8f4001f9..321e35486 100644 --- a/subworkflows/hicap/tests/nextflow.config +++ b/subworkflows/hicap/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of HICAP nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico cap locus typing of H. influenzae" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/hpsuissero/tests/main.nf.test.snap b/subworkflows/hpsuissero/tests/main.nf.test.snap index 322785506..e71e00f91 100644 --- a/subworkflows/hpsuissero/tests/main.nf.test.snap +++ b/subworkflows/hpsuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-04-29T11:18:19.038869937", + "timestamp": "2026-07-28T17:06:28.284182837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hpsuissero/tests/nextflow.config b/subworkflows/hpsuissero/tests/nextflow.config index 15c812a44..cb1756fb4 100644 --- a/subworkflows/hpsuissero/tests/nextflow.config +++ b/subworkflows/hpsuissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of HPSUISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Serotype prediction of Haemophilus parasuis" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/iqtree/tests/main.nf.test.snap b/subworkflows/iqtree/tests/main.nf.test.snap index 5c84b331b..8eec959ed 100644 --- a/subworkflows/iqtree/tests/main.nf.test.snap +++ b/subworkflows/iqtree/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "run" }, [ - "versions.yml:md5,e01256842798c2b435032141a36e34a4" + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f" ] ], - "timestamp": "2026-04-29T11:18:25.12719433", + "timestamp": "2026-07-28T17:06:33.455698419", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/iqtree/tests/nextflow.config b/subworkflows/iqtree/tests/nextflow.config index da69c602a..be3dcb3ed 100644 --- a/subworkflows/iqtree/tests/nextflow.config +++ b/subworkflows/iqtree/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of IQTREE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Maximum likelihood phylogenetic analysis" ext = "aln" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/iqtree/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ismapper/tests/main.nf.test.snap b/subworkflows/ismapper/tests/main.nf.test.snap index b2016d504..94f8716c0 100644 --- a/subworkflows/ismapper/tests/main.nf.test.snap +++ b/subworkflows/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-04-29T11:19:34.723180074", + "timestamp": "2026-07-28T17:07:44.514397831", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ismapper/tests/nextflow.config b/subworkflows/ismapper/tests/nextflow.config index a1c26e792..e577bf125 100644 --- a/subworkflows/ismapper/tests/nextflow.config +++ b/subworkflows/ismapper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ISMAPPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Insertion sequence mapping" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/ismapper/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/kleborate/tests/main.nf.test.snap b/subworkflows/kleborate/tests/main.nf.test.snap index 8b8c9d1bc..900cf1b3a 100644 --- a/subworkflows/kleborate/tests/main.nf.test.snap +++ b/subworkflows/kleborate/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-04-29T11:18:56.739504497", + "timestamp": "2026-07-28T17:07:05.900039873", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kleborate/tests/nextflow.config b/subworkflows/kleborate/tests/nextflow.config index 77231e301..84f2c5b23 100644 --- a/subworkflows/kleborate/tests/nextflow.config +++ b/subworkflows/kleborate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of KLEBORATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Screening of Klebsiella genome assemblies" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/kraken2/tests/main.nf.test.snap b/subworkflows/kraken2/tests/main.nf.test.snap index af04065dc..e2f34b81a 100644 --- a/subworkflows/kraken2/tests/main.nf.test.snap +++ b/subworkflows/kraken2/tests/main.nf.test.snap @@ -12,10 +12,10 @@ }, "SRR2838702.kraken2.report.txt:md5,29a9ad9bb9b9b17a43e969f82c6e3e9f", [ - "versions.yml:md5,64abaf13d756f2c9443d3b814985e107" + "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-04-29T11:18:54.186202424", + "timestamp": "2026-07-28T17:07:11.030883655", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kraken2/tests/nextflow.config b/subworkflows/kraken2/tests/nextflow.config index e7805dd59..2a52eff9f 100644 --- a/subworkflows/kraken2/tests/nextflow.config +++ b/subworkflows/kraken2/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of KRAKEN2 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Taxonomic classification of reads" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/kraken2/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/legsta/tests/main.nf.test.snap b/subworkflows/legsta/tests/main.nf.test.snap index 4ae8f7aac..852d36f3c 100644 --- a/subworkflows/legsta/tests/main.nf.test.snap +++ b/subworkflows/legsta/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-04-29T11:18:34.859965515", + "timestamp": "2026-07-28T17:06:49.435996446", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/legsta/tests/nextflow.config b/subworkflows/legsta/tests/nextflow.config index 9c3349558..7cb9bff09 100644 --- a/subworkflows/legsta/tests/nextflow.config +++ b/subworkflows/legsta/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of LEGSTA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico Legionella pneumophila Sequence Based Typing" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/lissero/tests/main.nf.test.snap b/subworkflows/lissero/tests/main.nf.test.snap index 76160d4f0..4c11a75b3 100644 --- a/subworkflows/lissero/tests/main.nf.test.snap +++ b/subworkflows/lissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-04-29T11:18:39.706405826", + "timestamp": "2026-07-28T17:06:54.015665013", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/lissero/tests/nextflow.config b/subworkflows/lissero/tests/nextflow.config index 3fc4be87f..c6d51ac8a 100644 --- a/subworkflows/lissero/tests/nextflow.config +++ b/subworkflows/lissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of LISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico serotyping of Listeria monocytogenes" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mashdist/tests/main.nf.test.snap b/subworkflows/mashdist/tests/main.nf.test.snap index 1676438ee..206186f19 100644 --- a/subworkflows/mashdist/tests/main.nf.test.snap +++ b/subworkflows/mashdist/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,fa387a5652585c181be4884eb12f37b0" ] ], - "timestamp": "2026-04-29T11:18:36.780964862", + "timestamp": "2026-07-28T17:06:59.318642745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashdist/tests/nextflow.config b/subworkflows/mashdist/tests/nextflow.config index 58a3ca1b9..9c284894d 100644 --- a/subworkflows/mashdist/tests/nextflow.config +++ b/subworkflows/mashdist/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MASHDIST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Calculate Mash distances between sequences" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mashtree/tests/main.nf.test.snap b/subworkflows/mashtree/tests/main.nf.test.snap index d404ac84e..8bf062b3b 100644 --- a/subworkflows/mashtree/tests/main.nf.test.snap +++ b/subworkflows/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8cd0c9b6f670d5ae21fda6592e85d32" ] ], - "timestamp": "2026-04-29T11:18:40.057093321", + "timestamp": "2026-07-28T17:06:59.284666206", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashtree/tests/nextflow.config b/subworkflows/mashtree/tests/nextflow.config index 1fa446447..c7d72e3cf 100644 --- a/subworkflows/mashtree/tests/nextflow.config +++ b/subworkflows/mashtree/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MASHTREE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Create a tree using Mash distances" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/mashtree/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mcroni/tests/main.nf.test.snap b/subworkflows/mcroni/tests/main.nf.test.snap index 74a4491d4..c8f6a067b 100644 --- a/subworkflows/mcroni/tests/main.nf.test.snap +++ b/subworkflows/mcroni/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,6eecf339ecef6511e62beca33a4b3fc6" ] ], - "timestamp": "2026-04-29T11:18:50.133272766", + "timestamp": "2026-07-28T17:07:03.359354314", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mcroni/tests/nextflow.config b/subworkflows/mcroni/tests/nextflow.config index 92b46f267..ad3450ae2 100644 --- a/subworkflows/mcroni/tests/nextflow.config +++ b/subworkflows/mcroni/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MCRONI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Sequence variation in mcr-1 bearing plasmids" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/meningotype/tests/main.nf.test.snap b/subworkflows/meningotype/tests/main.nf.test.snap index 560502e0a..0b3b367a0 100644 --- a/subworkflows/meningotype/tests/main.nf.test.snap +++ b/subworkflows/meningotype/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2210210917992673f792050a55c95b2e" ] ], - "timestamp": "2026-04-29T11:18:51.444103279", + "timestamp": "2026-07-28T17:07:04.025549387", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/meningotype/tests/nextflow.config b/subworkflows/meningotype/tests/nextflow.config index 81ff41fac..f7b04c290 100644 --- a/subworkflows/meningotype/tests/nextflow.config +++ b/subworkflows/meningotype/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MENINGOTYPE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Serotyping of Neisseria meningitidis" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/merlin/tests/main.nf.test b/subworkflows/merlin/tests/main.nf.test index 219bcc192..a7f344669 100644 --- a/subworkflows/merlin/tests/main.nf.test +++ b/subworkflows/merlin/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_workflow { input[4] = null input[5] = null input[6] = null + input[7] = null """ } } diff --git a/subworkflows/merlin/tests/nextflow.config b/subworkflows/merlin/tests/nextflow.config index 80e6ecbcf..d5228213a 100644 --- a/subworkflows/merlin/tests/nextflow.config +++ b/subworkflows/merlin/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MERLIN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Species-specific typing via Mash distance" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -55,13 +42,9 @@ includeConfig "../../../modules/tbprofiler/collate/module.config" includeConfig "../../../modules/agrvate/module.config" includeConfig "../../../modules/spatyper/module.config" includeConfig "../../../modules/sccmec/module.config" +includeConfig "../../../modules/staphscan/module.config" includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/merlindist/tests/main.nf.test.snap b/subworkflows/merlindist/tests/main.nf.test.snap index c84bb6cf9..f47c21365 100644 --- a/subworkflows/merlindist/tests/main.nf.test.snap +++ b/subworkflows/merlindist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,a714676ea5e603813de6640079a3f847" ] ], - "timestamp": "2026-04-29T11:20:03.900973384", + "timestamp": "2026-07-28T17:08:20.492381982", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/merlindist/tests/nextflow.config b/subworkflows/merlindist/tests/nextflow.config index 4ac50872b..8cac69c76 100644 --- a/subworkflows/merlindist/tests/nextflow.config +++ b/subworkflows/merlindist/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MERLINDIST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Species identification via Mash distances" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/merlin/dist/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/midas/tests/main.nf.test.snap b/subworkflows/midas/tests/main.nf.test.snap index 975c974ba..bdc5b75c5 100644 --- a/subworkflows/midas/tests/main.nf.test.snap +++ b/subworkflows/midas/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,66c2179f6d22e371b66b5d12ec5b0af1" ] ], - "timestamp": "2026-04-29T11:26:15.831138628", + "timestamp": "2026-07-28T17:14:25.322217018", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/midas/tests/nextflow.config b/subworkflows/midas/tests/nextflow.config index e06173209..4160a2cb5 100644 --- a/subworkflows/midas/tests/nextflow.config +++ b/subworkflows/midas/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MIDAS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Metagenomic Intra-species Diversity Analysis" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mlst/tests/main.nf.test.snap b/subworkflows/mlst/tests/main.nf.test.snap index e10b99110..4f3991be4 100644 --- a/subworkflows/mlst/tests/main.nf.test.snap +++ b/subworkflows/mlst/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_000017085.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6", [ - "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee" + "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e" ], { "id": "mlst-MLST:CSVTK_CONCAT", @@ -25,7 +25,7 @@ "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-04-29T11:19:20.491288912", + "timestamp": "2026-07-28T17:07:32.707561881", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mlst/tests/nextflow.config b/subworkflows/mlst/tests/nextflow.config index 6611b68e8..ed49e43ea 100644 --- a/subworkflows/mlst/tests/nextflow.config +++ b/subworkflows/mlst/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MLST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Multi-Locus Sequence Typing" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mobsuite/tests/main.nf.test.snap b/subworkflows/mobsuite/tests/main.nf.test.snap index 402199b25..88623cd4b 100644 --- a/subworkflows/mobsuite/tests/main.nf.test.snap +++ b/subworkflows/mobsuite/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,e586a98fe29a48792ce661d2649ada18" ] ], - "timestamp": "2026-04-29T11:20:32.622459663", + "timestamp": "2026-07-28T17:08:35.407292884", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mobsuite/tests/nextflow.config b/subworkflows/mobsuite/tests/nextflow.config index 1467a0187..bcfc8a60c 100644 --- a/subworkflows/mobsuite/tests/nextflow.config +++ b/subworkflows/mobsuite/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MOBSUITE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Reconstruct and annotate plasmids in draft assemblies" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/mykrobe/tests/main.nf.test.snap b/subworkflows/mykrobe/tests/main.nf.test.snap index e1f1021d9..315c9a0cc 100644 --- a/subworkflows/mykrobe/tests/main.nf.test.snap +++ b/subworkflows/mykrobe/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-04-29T11:19:25.950112659", + "timestamp": "2026-07-28T17:07:32.136787338", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mykrobe/tests/nextflow.config b/subworkflows/mykrobe/tests/nextflow.config index 92c25d53c..328871eb7 100644 --- a/subworkflows/mykrobe/tests/nextflow.config +++ b/subworkflows/mykrobe/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of MYKROBE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Antimicrobial resistance prediction" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ngmaster/tests/main.nf.test.snap b/subworkflows/ngmaster/tests/main.nf.test.snap index 055ceb63b..b8c9ccf66 100644 --- a/subworkflows/ngmaster/tests/main.nf.test.snap +++ b/subworkflows/ngmaster/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_001047255.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219", [ - "versions.yml:md5,dcc7b71de52c4fe65e10147be956aa05" + "versions.yml:md5,67ed215f25e8d088f830fb7d63ab9df5" ], { "id": "ngmaster-NGMASTER:CSVTK_CONCAT", @@ -25,7 +25,7 @@ "versions.yml:md5,9dbc0e8b7902e955ec10c94c11074f06" ] ], - "timestamp": "2026-04-29T11:19:44.012480256", + "timestamp": "2026-07-28T17:07:37.950807411", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ngmaster/tests/nextflow.config b/subworkflows/ngmaster/tests/nextflow.config index 6deafb497..64927ecf1 100644 --- a/subworkflows/ngmaster/tests/nextflow.config +++ b/subworkflows/ngmaster/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of NGMASTER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Multi-antigen sequence typing of Neisseria gonorrhoeae" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/nohuman/tests/main.nf.test.snap b/subworkflows/nohuman/tests/main.nf.test.snap index eb213570a..e19d4d6a5 100644 --- a/subworkflows/nohuman/tests/main.nf.test.snap +++ b/subworkflows/nohuman/tests/main.nf.test.snap @@ -12,10 +12,10 @@ "single_end": false }, [ - "versions.yml:md5,c7ccc6b38aecf3c08c8bc7c50814a452" + "versions.yml:md5,75d067d7ecc44ec6c90a321b8103c997" ] ], - "timestamp": "2026-04-29T11:24:05.709375483", + "timestamp": "2026-07-28T17:12:19.114645996", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/nohuman/tests/nextflow.config b/subworkflows/nohuman/tests/nextflow.config index 03c7bcc1f..a36cf1ddf 100644 --- a/subworkflows/nohuman/tests/nextflow.config +++ b/subworkflows/nohuman/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of NOHUMAN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Remove human reads from sequencing data" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for ALL processes used by this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/nohuman/download/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/panaroo/tests/main.nf.test.snap b/subworkflows/panaroo/tests/main.nf.test.snap index ef2b2c328..b73fb5852 100644 --- a/subworkflows/panaroo/tests/main.nf.test.snap +++ b/subworkflows/panaroo/tests/main.nf.test.snap @@ -10,10 +10,10 @@ "scope": "run" }, [ - "versions.yml:md5,6718c12232ea2c193a98b9723d0a2791" + "versions.yml:md5,0e38cb68a88a1a2911e751e9a8ffd648" ] ], - "timestamp": "2026-04-29T11:21:04.223957933", + "timestamp": "2026-07-28T17:09:10.973777305", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/panaroo/tests/nextflow.config b/subworkflows/panaroo/tests/nextflow.config index e07577ef5..4d4f3b047 100644 --- a/subworkflows/panaroo/tests/nextflow.config +++ b/subworkflows/panaroo/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PANAROO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pan-genome analysis with error correction" ext = "gff" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/panaroo/run/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/pangenome/tests/main.nf.test.snap b/subworkflows/pangenome/tests/main.nf.test.snap index 76da74e4b..f9f26192b 100644 --- a/subworkflows/pangenome/tests/main.nf.test.snap +++ b/subworkflows/pangenome/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "run" }, [ - "versions.yml:md5,5514295ba35a95ebb8417acd05766159" + "versions.yml:md5,709f42df442c9f6cc5132ad147bd334e" ], { "id": "core-genome.distance-snpdists", @@ -24,7 +24,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:21:06.006285694", + "timestamp": "2026-07-28T17:09:12.677207098", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pangenome/tests/nextflow.config b/subworkflows/pangenome/tests/nextflow.config index 8dbc7a04f..19a2abfdf 100644 --- a/subworkflows/pangenome/tests/nextflow.config +++ b/subworkflows/pangenome/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PANGENOME nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pan-genome analysis with multiple tools" ext = "gff" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -35,8 +22,3 @@ includeConfig "../../../modules/snpdists/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/pasty/tests/main.nf.test.snap b/subworkflows/pasty/tests/main.nf.test.snap index cd047518f..b80d09d0c 100644 --- a/subworkflows/pasty/tests/main.nf.test.snap +++ b/subworkflows/pasty/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,d806f451289eb221f11075799712603e" ] ], - "timestamp": "2026-04-29T11:19:34.599267238", + "timestamp": "2026-07-28T17:07:49.736137256", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pasty/tests/nextflow.config b/subworkflows/pasty/tests/nextflow.config index 3a233617e..44ecfbbe7 100644 --- a/subworkflows/pasty/tests/nextflow.config +++ b/subworkflows/pasty/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PASTY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico serogrouping of Pseudomonas aeruginosa" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/pbptyper/tests/main.nf.test.snap b/subworkflows/pbptyper/tests/main.nf.test.snap index 355d8e616..6aa951685 100644 --- a/subworkflows/pbptyper/tests/main.nf.test.snap +++ b/subworkflows/pbptyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18" ] ], - "timestamp": "2026-04-29T11:20:06.049259888", + "timestamp": "2026-07-28T17:08:16.195397015", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pbptyper/tests/nextflow.config b/subworkflows/pbptyper/tests/nextflow.config index d9c0c9ddc..c7cdf49e8 100644 --- a/subworkflows/pbptyper/tests/nextflow.config +++ b/subworkflows/pbptyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PBPTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "In silico PBP typing of Streptococcus pneumoniae" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/phispy/tests/main.nf.test.snap b/subworkflows/phispy/tests/main.nf.test.snap index 80d2771da..5c699c1e4 100644 --- a/subworkflows/phispy/tests/main.nf.test.snap +++ b/subworkflows/phispy/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "sample" }, [ - "versions.yml:md5,6487fa342391eda548b492a099ee91ed" + "versions.yml:md5,5e1425957e8a8025744f6a4d4dbb24cf" ], { "id": "phispy-PHISPY:CSVTK_CONCAT", @@ -24,7 +24,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-04-29T11:21:53.943104496", + "timestamp": "2026-07-28T17:10:00.907077676", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/phispy/tests/nextflow.config b/subworkflows/phispy/tests/nextflow.config index e19e5a2d8..9a05308f7 100644 --- a/subworkflows/phispy/tests/nextflow.config +++ b/subworkflows/phispy/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PHISPY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Prophage identification in bacterial genomes" ext = "gbk" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/pirate/tests/main.nf.test.snap b/subworkflows/pirate/tests/main.nf.test.snap index 6e0577624..3bcbc31c4 100644 --- a/subworkflows/pirate/tests/main.nf.test.snap +++ b/subworkflows/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,424257d69beae21355dee29eac16ca77" ] ], - "timestamp": "2026-04-29T11:22:26.662137554", + "timestamp": "2026-07-28T17:10:36.275704573", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pirate/tests/nextflow.config b/subworkflows/pirate/tests/nextflow.config index 50c2dd390..4548d6cdd 100644 --- a/subworkflows/pirate/tests/nextflow.config +++ b/subworkflows/pirate/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PIRATE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pangenome analysis and threshold evaluation" ext = "gff" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/pirate/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/plasmidfinder/tests/main.nf.test.snap b/subworkflows/plasmidfinder/tests/main.nf.test.snap index 7f075128a..d20f88560 100644 --- a/subworkflows/plasmidfinder/tests/main.nf.test.snap +++ b/subworkflows/plasmidfinder/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-04-29T11:19:45.384910888", + "timestamp": "2026-07-28T17:07:55.903861211", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/plasmidfinder/tests/nextflow.config b/subworkflows/plasmidfinder/tests/nextflow.config index 54d0b2e67..936b3573a 100644 --- a/subworkflows/plasmidfinder/tests/nextflow.config +++ b/subworkflows/plasmidfinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PLASMIDFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Identification of plasmids in bacterial sequences" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/pneumocat/tests/main.nf.test.snap b/subworkflows/pneumocat/tests/main.nf.test.snap index a7a7fe895..f3573f2e8 100644 --- a/subworkflows/pneumocat/tests/main.nf.test.snap +++ b/subworkflows/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-04-29T11:20:04.755813798", + "timestamp": "2026-07-28T17:08:14.3721084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pneumocat/tests/nextflow.config b/subworkflows/pneumocat/tests/nextflow.config index 3626afe48..719435be2 100644 --- a/subworkflows/pneumocat/tests/nextflow.config +++ b/subworkflows/pneumocat/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PNEUMOCAT nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pneumococcal capsular typing from reads" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/pneumocat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/prokka/tests/main.nf.test.snap b/subworkflows/prokka/tests/main.nf.test.snap index 70af7edae..06ee957a6 100644 --- a/subworkflows/prokka/tests/main.nf.test.snap +++ b/subworkflows/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-04-29T11:19:54.417731097", + "timestamp": "2026-07-28T17:08:04.569776837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/prokka/tests/nextflow.config b/subworkflows/prokka/tests/nextflow.config index b5e731197..ce120e650 100644 --- a/subworkflows/prokka/tests/nextflow.config +++ b/subworkflows/prokka/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of PROKKA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,23 +10,9 @@ params { description = "Rapid prokaryotic genome annotation" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" // Under nf-test, projectDir is this tests/ directory bactopia_dir = "${projectDir}/../../.." - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/prokka/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/quast/tests/main.nf.test.snap b/subworkflows/quast/tests/main.nf.test.snap index 726d4bfe4..d321b76d6 100644 --- a/subworkflows/quast/tests/main.nf.test.snap +++ b/subworkflows/quast/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6625779099decc901ee6311371b1230" ] ], - "timestamp": "2026-04-29T11:19:50.023328945", + "timestamp": "2026-07-28T17:08:00.903619665", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/quast/tests/nextflow.config b/subworkflows/quast/tests/nextflow.config index 4726b4414..7801d8151 100644 --- a/subworkflows/quast/tests/nextflow.config +++ b/subworkflows/quast/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of QUAST nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Quality assessment of genome assemblies" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/rgi/tests/main.nf.test.snap b/subworkflows/rgi/tests/main.nf.test.snap index e7726ac15..23dbcdef0 100644 --- a/subworkflows/rgi/tests/main.nf.test.snap +++ b/subworkflows/rgi/tests/main.nf.test.snap @@ -9,9 +9,9 @@ "process_name": "rgi_main", "scope": "sample" }, - "GCF_900478275.tsv:md5,9d7754551163e020beed52a8bc14ce83", + "GCF_900478275.tsv:md5,9dd0afe6946da9c6608e775f954813a1", [ - "versions.yml:md5,4a19310417d04abb9e1eeec05629f944" + "versions.yml:md5,6a43ca3ba925940f762a035f862fc657" ], { "id": "rgi-RGI:CSVTK_CONCAT", @@ -25,7 +25,7 @@ "versions.yml:md5,c1294552ba205b057bd368875a4eac93" ] ], - "timestamp": "2026-04-29T11:20:52.07740056", + "timestamp": "2026-07-28T18:35:33.791763973", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/rgi/tests/nextflow.config b/subworkflows/rgi/tests/nextflow.config index 5b1c2eeeb..53b8559f7 100644 --- a/subworkflows/rgi/tests/nextflow.config +++ b/subworkflows/rgi/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of RGI nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Resistance Gene Identifier" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/roary/tests/main.nf.test.snap b/subworkflows/roary/tests/main.nf.test.snap index da8924638..2a2d1f1ae 100644 --- a/subworkflows/roary/tests/main.nf.test.snap +++ b/subworkflows/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d5496a62b5ffe9e5af444bfc53221551" ] ], - "timestamp": "2026-04-29T11:21:14.562495592", + "timestamp": "2026-07-28T17:09:14.970364044", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/roary/tests/nextflow.config b/subworkflows/roary/tests/nextflow.config index 0fe2597e7..08661b91a 100644 --- a/subworkflows/roary/tests/nextflow.config +++ b/subworkflows/roary/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of ROARY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Rapid large-scale prokaryote pan genome analysis" ext = "gff" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/roary/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/sccmec/tests/main.nf.test.snap b/subworkflows/sccmec/tests/main.nf.test.snap index 5ae0a6f61..37da3637d 100644 --- a/subworkflows/sccmec/tests/main.nf.test.snap +++ b/subworkflows/sccmec/tests/main.nf.test.snap @@ -29,7 +29,7 @@ "versions.yml:md5,c6ede7b0533855a33c127cafa29de747" ] ], - "timestamp": "2026-04-29T11:20:09.177950088", + "timestamp": "2026-07-28T17:08:04.469024676", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sccmec/tests/nextflow.config b/subworkflows/sccmec/tests/nextflow.config index 63fe4a812..469738434 100644 --- a/subworkflows/sccmec/tests/nextflow.config +++ b/subworkflows/sccmec/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SCCMEC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "SCCmec typing of Staphylococcus aureus" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/scoary/tests/main.nf.test.snap b/subworkflows/scoary/tests/main.nf.test.snap index 833cf8a38..9c3adce13 100644 --- a/subworkflows/scoary/tests/main.nf.test.snap +++ b/subworkflows/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,36d9b366d4941f258a248bf7a31aecc7" ] ], - "timestamp": "2026-04-29T11:20:05.143988308", + "timestamp": "2026-07-28T17:08:12.639645628", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scoary/tests/nextflow.config b/subworkflows/scoary/tests/nextflow.config index 5145b6a80..68bea521d 100644 --- a/subworkflows/scoary/tests/nextflow.config +++ b/subworkflows/scoary/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SCOARY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pan-genome-wide association studies" ext = "csv" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/scoary/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/scrubber/tests/main.nf.test.snap b/subworkflows/scrubber/tests/main.nf.test.snap index 9aadd8252..468b1ec22 100644 --- a/subworkflows/scrubber/tests/main.nf.test.snap +++ b/subworkflows/scrubber/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "scrubber - subworkflow - SRR2838702": { + "scrubber - subworkflow - SRR2838702 - nohuman": { "content": [ { "id": "SRR2838702-SCRUBBER:NOHUMAN:NOHUMAN_MODULE", @@ -12,7 +12,7 @@ "single_end": false }, [ - "versions.yml:md5,a8320e62273b53dca9cfffcb088d3ebb" + "versions.yml:md5,02561307297f583bd0d158052302fcf0" ], { "id": "scrubber-SCRUBBER:CSVTK_CONCAT", @@ -26,7 +26,40 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-04-29T11:25:01.657945097", + "timestamp": "2026-07-28T17:13:10.124789088", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "scrubber - subworkflow - SRR2838702 - deacon": { + "content": [ + { + "id": "SRR2838702-SCRUBBER:DEACON:DEACON_MODULE", + "logs_dir": "SRR2838702/tools/scrubber/logs/", + "name": "SRR2838702", + "output_dir": "SRR2838702/tools/scrubber", + "process_name": "deacon", + "runtype": "paired-end", + "scope": "sample", + "single_end": false + }, + [ + "versions.yml:md5,e07f44b8fe13644174f75b5cc7193f10" + ], + { + "id": "scrubber-SCRUBBER:CSVTK_CONCAT", + "logs_dir": "merged-results/logs/scrubber-concat/", + "name": "scrubber", + "output_dir": "merged-results", + "process_name": "scrubber-concat", + "scope": "run" + }, + [ + "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" + ] + ], + "timestamp": "2026-07-28T17:13:48.231768727", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scrubber/tests/nextflow.config b/subworkflows/scrubber/tests/nextflow.config index a0db097db..ac492ff12 100644 --- a/subworkflows/scrubber/tests/nextflow.config +++ b/subworkflows/scrubber/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SCRUBBER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Host read removal" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Nohuman params (used when use_srascrubber = false) nohuman_db = "${params.test_data_dir}/datasets/nohuman/HPRC.r2" @@ -43,8 +30,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/seqsero2/tests/main.nf.test.snap b/subworkflows/seqsero2/tests/main.nf.test.snap index 7257097b6..886d9d79d 100644 --- a/subworkflows/seqsero2/tests/main.nf.test.snap +++ b/subworkflows/seqsero2/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-04-29T11:20:11.602680544", + "timestamp": "2026-07-28T17:08:21.120755", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seqsero2/tests/nextflow.config b/subworkflows/seqsero2/tests/nextflow.config index 2b625e033..c2ec5e982 100644 --- a/subworkflows/seqsero2/tests/nextflow.config +++ b/subworkflows/seqsero2/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SEQSERO2 nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Salmonella serotype determination" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/seroba/tests/main.nf.test.snap b/subworkflows/seroba/tests/main.nf.test.snap index e40f44c00..8808d758a 100644 --- a/subworkflows/seroba/tests/main.nf.test.snap +++ b/subworkflows/seroba/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,4fd4f724e2f19016eff39a2b524a9007" ] ], - "timestamp": "2026-04-29T11:21:01.497216213", + "timestamp": "2026-07-28T17:09:07.672344725", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seroba/tests/nextflow.config b/subworkflows/seroba/tests/nextflow.config index 19fe2d42f..d90b833f5 100644 --- a/subworkflows/seroba/tests/nextflow.config +++ b/subworkflows/seroba/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SEROBA nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Serotyping of Streptococcus pneumoniae from reads" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/shigapass/tests/main.nf.test.snap b/subworkflows/shigapass/tests/main.nf.test.snap index c18ff1eb2..bf9defdd4 100644 --- a/subworkflows/shigapass/tests/main.nf.test.snap +++ b/subworkflows/shigapass/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f481607e2b7526fd798b2375bb3cc9c4" ] ], - "timestamp": "2026-04-29T11:20:24.235477607", + "timestamp": "2026-07-28T17:08:32.362126691", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigapass/tests/nextflow.config b/subworkflows/shigapass/tests/nextflow.config index 55ee50fda..8e82f8766 100644 --- a/subworkflows/shigapass/tests/nextflow.config +++ b/subworkflows/shigapass/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SHIGAPASS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Shigella serotyping from assemblies" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/shigatyper/tests/main.nf.test.snap b/subworkflows/shigatyper/tests/main.nf.test.snap index 5d916f968..d999d7fb3 100644 --- a/subworkflows/shigatyper/tests/main.nf.test.snap +++ b/subworkflows/shigatyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-04-29T11:20:18.516664959", + "timestamp": "2026-07-28T17:08:26.895571966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigatyper/tests/nextflow.config b/subworkflows/shigatyper/tests/nextflow.config index 6902b7330..5b6b839b5 100644 --- a/subworkflows/shigatyper/tests/nextflow.config +++ b/subworkflows/shigatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SHIGATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Shigella serotyping from reads" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/shigeifinder/tests/main.nf.test.snap b/subworkflows/shigeifinder/tests/main.nf.test.snap index 6b196be3a..c12adc347 100644 --- a/subworkflows/shigeifinder/tests/main.nf.test.snap +++ b/subworkflows/shigeifinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,bb067649d1cb0b7cc78ced0baa36bf0e" ] ], - "timestamp": "2026-04-29T11:20:18.806924242", + "timestamp": "2026-07-28T17:08:24.034447868", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigeifinder/tests/nextflow.config b/subworkflows/shigeifinder/tests/nextflow.config index 6a508232d..b9af16118 100644 --- a/subworkflows/shigeifinder/tests/nextflow.config +++ b/subworkflows/shigeifinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SHIGEIFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Shigella and EIEC serotype identification" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/sistr/tests/main.nf.test.snap b/subworkflows/sistr/tests/main.nf.test.snap index 9cf6f7154..650e7a3da 100644 --- a/subworkflows/sistr/tests/main.nf.test.snap +++ b/subworkflows/sistr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-04-29T11:20:54.656801118", + "timestamp": "2026-07-28T17:08:53.346594316", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sistr/tests/nextflow.config b/subworkflows/sistr/tests/nextflow.config index 3c684a198..a9e4ef673 100644 --- a/subworkflows/sistr/tests/nextflow.config +++ b/subworkflows/sistr/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SISTR nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Serovar predictions for Salmonella species" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/snippy/core/tests/main.nf.test.snap b/subworkflows/snippy/core/tests/main.nf.test.snap index 4d86ae056..2a8b4287d 100644 --- a/subworkflows/snippy/core/tests/main.nf.test.snap +++ b/subworkflows/snippy/core/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:20:33.46198183", + "timestamp": "2026-07-28T17:08:31.929234822", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/core/tests/nextflow.config b/subworkflows/snippy/core/tests/nextflow.config index e42a5908d..695be9b00 100644 --- a/subworkflows/snippy/core/tests/nextflow.config +++ b/subworkflows/snippy/core/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SNIPPY_CORE nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Core SNP alignment from Snippy outputs" ext = "aln" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults skip_compression = false @@ -36,8 +23,3 @@ includeConfig "../../../../modules/snpdists/module.config" // Base config (container resolution + resource labels) includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/snippy/run/tests/main.nf.test.snap b/subworkflows/snippy/run/tests/main.nf.test.snap index b08f68bf3..e3a51d5ce 100644 --- a/subworkflows/snippy/run/tests/main.nf.test.snap +++ b/subworkflows/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30" ] ], - "timestamp": "2026-04-29T11:21:00.828251895", + "timestamp": "2026-07-28T17:08:59.258337174", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/run/tests/nextflow.config b/subworkflows/snippy/run/tests/nextflow.config index 3e48f2928..ce42ee3cd 100644 --- a/subworkflows/snippy/run/tests/nextflow.config +++ b/subworkflows/snippy/run/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SNIPPY nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Variant calling from reads against a reference" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" // Module-specific defaults skip_compression = false @@ -35,8 +22,3 @@ includeConfig "../../../../modules/snippy/run/module.config" // Base config (container resolution + resource labels) includeConfig "../../../../conf/base.config" includeConfig "../../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/snpdists/tests/main.nf.test.snap b/subworkflows/snpdists/tests/main.nf.test.snap index bfa2ca447..32765019e 100644 --- a/subworkflows/snpdists/tests/main.nf.test.snap +++ b/subworkflows/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b7c9ec6305cc1637c144c82ba20a94d6" ] ], - "timestamp": "2026-04-29T11:20:37.293805741", + "timestamp": "2026-07-28T17:08:34.105236475", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snpdists/tests/nextflow.config b/subworkflows/snpdists/tests/nextflow.config index ae6f1e29d..70f3974fc 100644 --- a/subworkflows/snpdists/tests/nextflow.config +++ b/subworkflows/snpdists/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SNPDISTS nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Pairwise SNP distance matrix from a FASTA alignment" ext = "aln" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -32,8 +19,3 @@ includeConfig "../../../modules/snpdists/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/spatyper/tests/main.nf.test.snap b/subworkflows/spatyper/tests/main.nf.test.snap index 0eb21b06b..390ef7c0b 100644 --- a/subworkflows/spatyper/tests/main.nf.test.snap +++ b/subworkflows/spatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2be001b7db8743258dd915dfe57337f4" ] ], - "timestamp": "2026-04-29T11:20:47.919788605", + "timestamp": "2026-07-28T17:08:45.698763094", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/spatyper/tests/nextflow.config b/subworkflows/spatyper/tests/nextflow.config index 440532f20..b2e5d2b5f 100644 --- a/subworkflows/spatyper/tests/nextflow.config +++ b/subworkflows/spatyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SPATYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Computational typing of spa repeats" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/srahumanscrubber/tests/main.nf.test.snap b/subworkflows/srahumanscrubber/tests/main.nf.test.snap index 649ff5a41..c0fd56be6 100644 --- a/subworkflows/srahumanscrubber/tests/main.nf.test.snap +++ b/subworkflows/srahumanscrubber/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,ca8ec5702526f2d59b7e3c5068c1c400" ] ], - "timestamp": "2026-04-29T11:21:28.474469716", + "timestamp": "2026-07-28T17:10:21.645824392", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/srahumanscrubber/tests/nextflow.config b/subworkflows/srahumanscrubber/tests/nextflow.config index 0e7e0a23e..bef149551 100644 --- a/subworkflows/srahumanscrubber/tests/nextflow.config +++ b/subworkflows/srahumanscrubber/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SRAHUMANSCRUBBER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Host read removal using SRA Human Scrubber" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/srahumanscrubber/scrub/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/ssuissero/tests/main.nf.test.snap b/subworkflows/ssuissero/tests/main.nf.test.snap index f92a28e65..63a8ff8b1 100644 --- a/subworkflows/ssuissero/tests/main.nf.test.snap +++ b/subworkflows/ssuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b273046b082dd70970b8f4e189aa5498" ] ], - "timestamp": "2026-04-29T11:20:47.810631649", + "timestamp": "2026-07-28T17:08:50.652379608", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ssuissero/tests/nextflow.config b/subworkflows/ssuissero/tests/nextflow.config index e39af0057..2fefd9e8d 100644 --- a/subworkflows/ssuissero/tests/nextflow.config +++ b/subworkflows/ssuissero/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SSUISSERO nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Serotype prediction of Streptococcus suis" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/staphopiasccmec/tests/main.nf.test.snap b/subworkflows/staphopiasccmec/tests/main.nf.test.snap index 9d8d2d3b8..134110449 100644 --- a/subworkflows/staphopiasccmec/tests/main.nf.test.snap +++ b/subworkflows/staphopiasccmec/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f59d6534316ffe1998c60f98b212d80f" ] ], - "timestamp": "2026-04-29T11:20:51.447164522", + "timestamp": "2026-07-28T17:08:50.647848823", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphopiasccmec/tests/nextflow.config b/subworkflows/staphopiasccmec/tests/nextflow.config index 3ec5964fc..85867db07 100644 --- a/subworkflows/staphopiasccmec/tests/nextflow.config +++ b/subworkflows/staphopiasccmec/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of STAPHOPIASCCMEC nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "SCCmec typing for Staphylococcus aureus" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/staphscan/tests/main.nf.test.snap b/subworkflows/staphscan/tests/main.nf.test.snap index 55c91a903..e175eae20 100644 --- a/subworkflows/staphscan/tests/main.nf.test.snap +++ b/subworkflows/staphscan/tests/main.nf.test.snap @@ -9,9 +9,9 @@ "process_name": "staphscan", "scope": "sample" }, - "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", + "GCF_000017085.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e", [ - "versions.yml:md5,21366a5b932268b20a58c129bf66d90b" + "versions.yml:md5,794f66edfdb0127b7c9b08a1bb6d3231" ], { "id": "staphscan-STAPHSCAN:CSVTK_CONCAT", @@ -25,7 +25,7 @@ "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b" ] ], - "timestamp": "2026-05-05T12:03:39.31515092", + "timestamp": "2026-07-28T17:09:05.015272733", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphscan/tests/nextflow.config b/subworkflows/staphscan/tests/nextflow.config index 295dacfea..ad0f82bf6 100644 --- a/subworkflows/staphscan/tests/nextflow.config +++ b/subworkflows/staphscan/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of STAPHSCAN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Genome-based surveillance analysis of Staphylococcus aureus" ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/staphtyper/tests/main.nf.test b/subworkflows/staphtyper/tests/main.nf.test index 7d2adee99..97a08e61d 100644 --- a/subworkflows/staphtyper/tests/main.nf.test +++ b/subworkflows/staphtyper/tests/main.nf.test @@ -20,6 +20,7 @@ nextflow_workflow { ) input[1] = null input[2] = null + input[3] = null """ } } diff --git a/subworkflows/staphtyper/tests/nextflow.config b/subworkflows/staphtyper/tests/nextflow.config index 8c199ac95..46534c66a 100644 --- a/subworkflows/staphtyper/tests/nextflow.config +++ b/subworkflows/staphtyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of STAPHTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,34 +10,16 @@ params { description = "S. aureus typing (agrvate + spatyper + sccmec)" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow includeConfig "../../../modules/agrvate/module.config" includeConfig "../../../modules/spatyper/module.config" includeConfig "../../../modules/sccmec/module.config" +includeConfig "../../../modules/staphscan/module.config" includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/stecfinder/main.nf b/subworkflows/stecfinder/main.nf index ad315601f..912641ac0 100644 --- a/subworkflows/stecfinder/main.nf +++ b/subworkflows/stecfinder/main.nf @@ -38,8 +38,7 @@ workflow STECFINDER { seqs: Channel main: - // If user passes --stecfinder_use_reads, we have to filter out any samples that - // have no reads. + // If user passes --stecfinder_use_reads, we have to filter out any samples without reads. def ch_seqs = (params.stecfinder_use_reads ? seqs.filter { r -> [r.r1, r.r2, r.se, r.lr].any { seq -> seq != null } } : seqs diff --git a/subworkflows/stecfinder/tests/main.nf.test.snap b/subworkflows/stecfinder/tests/main.nf.test.snap index 2675535b1..6a86d258d 100644 --- a/subworkflows/stecfinder/tests/main.nf.test.snap +++ b/subworkflows/stecfinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,a4e0bfe59670d712011a3dc00f3abeb5" ] ], - "timestamp": "2026-04-29T11:20:57.771873873", + "timestamp": "2026-07-28T17:09:02.440013767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stecfinder/tests/nextflow.config b/subworkflows/stecfinder/tests/nextflow.config index 4ac09faf4..59b6f6f6a 100644 --- a/subworkflows/stecfinder/tests/nextflow.config +++ b/subworkflows/stecfinder/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of STECFINDER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "STEC serotyping and virulence detection" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/stxtyper/tests/main.nf.test.snap b/subworkflows/stxtyper/tests/main.nf.test.snap index 1406ca6b6..6fa2221ce 100644 --- a/subworkflows/stxtyper/tests/main.nf.test.snap +++ b/subworkflows/stxtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c" ] ], - "timestamp": "2026-05-21T13:55:41.392691647", + "timestamp": "2026-07-28T17:09:05.058482264", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stxtyper/tests/nextflow.config b/subworkflows/stxtyper/tests/nextflow.config index 3746210c0..65152df7f 100644 --- a/subworkflows/stxtyper/tests/nextflow.config +++ b/subworkflows/stxtyper/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of STXTYPER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Identify and type Stx operons from assembled genomic sequences" ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.5' -} diff --git a/subworkflows/sylph/tests/main.nf.test.snap b/subworkflows/sylph/tests/main.nf.test.snap index 20c2c6642..33552d9e8 100644 --- a/subworkflows/sylph/tests/main.nf.test.snap +++ b/subworkflows/sylph/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2a85d1cd25d2a88c77d90030e05e17cf" ] ], - "timestamp": "2026-04-29T11:22:08.970225804", + "timestamp": "2026-07-28T17:10:11.454967252", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sylph/tests/nextflow.config b/subworkflows/sylph/tests/nextflow.config index 6f0473312..bd6bae64c 100644 --- a/subworkflows/sylph/tests/nextflow.config +++ b/subworkflows/sylph/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of SYLPH nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Ultra-fast taxonomic profiling" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/tblastn/tests/main.nf.test.snap b/subworkflows/tblastn/tests/main.nf.test.snap index 964fa6242..e2b2c0d15 100644 --- a/subworkflows/tblastn/tests/main.nf.test.snap +++ b/subworkflows/tblastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,413650f494aaf14a524501ce6dc5c959" ] ], - "timestamp": "2026-04-29T11:20:57.898688227", + "timestamp": "2026-07-28T17:09:01.958674812", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastn/tests/nextflow.config b/subworkflows/tblastn/tests/nextflow.config index c143cad0f..e2d33ff9f 100644 --- a/subworkflows/tblastn/tests/nextflow.config +++ b/subworkflows/tblastn/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of TBLASTN nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "BLAST tblastn search" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/tblastx/tests/main.nf.test.snap b/subworkflows/tblastx/tests/main.nf.test.snap index 7220bd41d..4a9df89f4 100644 --- a/subworkflows/tblastx/tests/main.nf.test.snap +++ b/subworkflows/tblastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8ebdf55bc992d797630ad6f81b6cbe3d" ] ], - "timestamp": "2026-04-29T11:21:01.772173648", + "timestamp": "2026-07-28T17:09:06.538184913", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastx/tests/nextflow.config b/subworkflows/tblastx/tests/nextflow.config index 322989a22..f02ff2e5a 100644 --- a/subworkflows/tblastx/tests/nextflow.config +++ b/subworkflows/tblastx/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of TBLASTX nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "BLAST tblastx search" ext = "fna" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/tbprofiler/tests/main.nf.test.snap b/subworkflows/tbprofiler/tests/main.nf.test.snap index a55e9c93a..8271c9036 100644 --- a/subworkflows/tbprofiler/tests/main.nf.test.snap +++ b/subworkflows/tbprofiler/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-04-29T11:22:01.745237267", + "timestamp": "2026-07-28T17:10:04.694119884", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tbprofiler/tests/nextflow.config b/subworkflows/tbprofiler/tests/nextflow.config index db03f2105..dae8ea1b8 100644 --- a/subworkflows/tbprofiler/tests/nextflow.config +++ b/subworkflows/tbprofiler/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of TBPROFILER nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Profiling of Mycobacterium tuberculosis" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -33,8 +20,3 @@ includeConfig "../../../modules/tbprofiler/collate/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/teton/tests/main.nf.test b/subworkflows/teton/tests/main.nf.test index aae8ce84e..f6be5db92 100644 --- a/subworkflows/teton/tests/main.nf.test +++ b/subworkflows/teton/tests/main.nf.test @@ -23,9 +23,12 @@ nextflow_workflow { ) input[1] = file("${params.test_data_dir}/datasets/kraken2/k2_standard_08_GB_20251015") input[2] = false - input[3] = file("${params.test_data_dir}/datasets/nohuman/HPRC.r2") - input[4] = false + input[3] = true + input[4] = file("${params.test_data_dir}/datasets/nohuman/HPRC.r2") input[5] = false + input[6] = false + input[7] = null + input[8] = false """ } } diff --git a/subworkflows/teton/tests/main.nf.test.snap b/subworkflows/teton/tests/main.nf.test.snap index b73729afc..dd7fd84fe 100644 --- a/subworkflows/teton/tests/main.nf.test.snap +++ b/subworkflows/teton/tests/main.nf.test.snap @@ -12,7 +12,7 @@ "single_end": false }, [ - "versions.yml:md5,0e919355c3b46201c37e019227934b1b" + "versions.yml:md5,14feb3b47ba66dc6b247bdd7debcc18c" ], { "id": "SRR2838702-TETON:BRACKEN:BRACKEN_MODULE", @@ -25,10 +25,10 @@ "teton_reads": "SRR2838702_R1.scrubbed.fastq.gz,SRR2838702_R2.scrubbed.fastq.gz" }, [ - "versions.yml:md5,8dc4d8979e0dba7fc7b975f9953a3161" + "versions.yml:md5,7d27773f1e349726172140b0c615a73b" ] ], - "timestamp": "2026-04-29T11:30:25.229414267", + "timestamp": "2026-07-28T18:48:22.978120925", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/teton/tests/nextflow.config b/subworkflows/teton/tests/nextflow.config index c870f0b33..71448a8c9 100644 --- a/subworkflows/teton/tests/nextflow.config +++ b/subworkflows/teton/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of TETON nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Meta-analysis of reads" ext = "fastq" } - bactopia_version = '4.0.0' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -39,8 +26,3 @@ includeConfig "../../../modules/bactopia/teton/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/subworkflows/traitar/tests/main.nf.test.snap b/subworkflows/traitar/tests/main.nf.test.snap index 2fa921560..c4c6813bc 100644 --- a/subworkflows/traitar/tests/main.nf.test.snap +++ b/subworkflows/traitar/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,0876b2d126e96f86b158fe8dddf4f05f" ] ], - "timestamp": "2026-05-06T08:40:48.418831853", + "timestamp": "2026-07-28T19:49:48.509801502", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/traitar/tests/nextflow.config b/subworkflows/traitar/tests/nextflow.config index 72b376705..ef1105525 100644 --- a/subworkflows/traitar/tests/nextflow.config +++ b/subworkflows/traitar/tests/nextflow.config @@ -1,6 +1,7 @@ // Minimal config for subworkflow-level testing of TRAITAR nextflow.enable.types = true nextflow.enable.strict = true +includeConfig "../../../conf/test_base.config" params { workflow { @@ -9,21 +10,7 @@ params { description = "Predict phenotypic traits from microbial genomes" ext = "fna" } - bactopia_version = '4.0.1' - bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" wf = params.workflow.name - merge_folder = "merged-results" - test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" - is_ci = true - max_retry = 1 - max_time = 2.h - max_memory = 8.GB - max_cpus = 2 - registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false - container_opts = "" } // Load module configs for processes in this subworkflow @@ -34,8 +21,3 @@ includeConfig "../../../modules/csvtk/concat/module.config" // Base config (container resolution + resource labels) includeConfig "../../../conf/base.config" includeConfig "../../../conf/profiles.config" - -// Plugin -plugins { - id 'nf-bactopia@2.1.6' -} diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 10e194ca5..58bf316ad 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -1,764 +1,4 @@ { - "Bactopia (se) - SRR2838702|portiera|illumina": { - "content": [ - 11, - [ - "SRR2838702", - "SRR2838702/main", - "SRR2838702/main/annotator", - "SRR2838702/main/annotator/prokka", - "SRR2838702/main/annotator/prokka/SRR2838702-blastdb.tar.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.faa.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.ffn.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.fna.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.fsa.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.gbk.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.gff.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.sqn.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.tbl.gz", - "SRR2838702/main/annotator/prokka/SRR2838702.tsv", - "SRR2838702/main/annotator/prokka/SRR2838702.txt", - "SRR2838702/main/annotator/prokka/logs", - "SRR2838702/main/annotator/prokka/logs/SRR2838702.err", - "SRR2838702/main/annotator/prokka/logs/SRR2838702.log", - "SRR2838702/main/annotator/prokka/logs/nf.command.begin", - "SRR2838702/main/annotator/prokka/logs/nf.command.err", - "SRR2838702/main/annotator/prokka/logs/nf.command.log", - "SRR2838702/main/annotator/prokka/logs/nf.command.out", - "SRR2838702/main/annotator/prokka/logs/nf.command.run", - "SRR2838702/main/annotator/prokka/logs/nf.command.sh", - "SRR2838702/main/annotator/prokka/logs/nf.command.trace", - "SRR2838702/main/annotator/prokka/logs/versions.yml", - "SRR2838702/main/assembler", - "SRR2838702/main/assembler/SRR2838702.fna.gz", - "SRR2838702/main/assembler/SRR2838702.tsv", - "SRR2838702/main/assembler/logs", - "SRR2838702/main/assembler/logs/nf.command.begin", - "SRR2838702/main/assembler/logs/nf.command.err", - "SRR2838702/main/assembler/logs/nf.command.log", - "SRR2838702/main/assembler/logs/nf.command.out", - "SRR2838702/main/assembler/logs/nf.command.run", - "SRR2838702/main/assembler/logs/nf.command.sh", - "SRR2838702/main/assembler/logs/nf.command.trace", - "SRR2838702/main/assembler/logs/shovill-se.log", - "SRR2838702/main/assembler/logs/versions.yml", - "SRR2838702/main/assembler/supplemental", - "SRR2838702/main/assembler/supplemental/illumina.txt", - "SRR2838702/main/assembler/supplemental/shovill.corrections", - "SRR2838702/main/gather", - "SRR2838702/main/gather/SRR2838702-meta.tsv", - "SRR2838702/main/gather/logs", - 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"bactopia-runs/bactopia/merged-results/logs/mlst-concat/nf.command.trace", - "bactopia-runs/bactopia/merged-results/logs/mlst-concat/versions.yml", - "bactopia-runs/bactopia/merged-results/meta.tsv", - "bactopia-runs/bactopia/merged-results/mlst.tsv", - "bactopia-runs/bactopia/nf-reports", - "bactopia-runs/bactopia/nf-reports/bactopia-dag.dot", - "bactopia-runs/bactopia/nf-reports/bactopia-report.html", - "bactopia-runs/bactopia/nf-reports/bactopia-timeline.html" - ], - [ - "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e", - "versions.yml:md5,5d00225a5ad24de728e651fdd0d7d1e3", - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", "versions.yml:md5,e46de3078794860a978e2dd0b390c27c", - "versions.yml:md5,d4aac41b9e2c72836a9b2a1dfed2226c", - "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee", + "versions.yml:md5,9ca3ec85a3c0993ed41a25321fd6d423", + "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e", "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6", "versions.yml:md5,1913efda4329af168df4ab88555dbeb4", "versions.yml:md5,61924107a406c136f55c445d470721f7", "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-04-29T11:39:34.253436144", + "timestamp": "2026-07-28T20:21:51.913874897", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1385,18 +374,18 @@ [ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e", "versions.yml:md5,5d00225a5ad24de728e651fdd0d7d1e3", - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", "versions.yml:md5,e46de3078794860a978e2dd0b390c27c", - "versions.yml:md5,d4aac41b9e2c72836a9b2a1dfed2226c", - "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee", + "versions.yml:md5,9ca3ec85a3c0993ed41a25321fd6d423", + "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e", "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6", "versions.yml:md5,1913efda4329af168df4ab88555dbeb4", "versions.yml:md5,61924107a406c136f55c445d470721f7", "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-04-29T11:27:11.243153114", + "timestamp": "2026-07-28T20:18:28.980338516", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/versions.yml b/versions.yml new file mode 100644 index 000000000..2823bbcd1 --- /dev/null +++ b/versions.yml @@ -0,0 +1,2 @@ +bactopia: 4.1.0 +nf-bactopia: 2.1.6 diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index 3d09126ad..a7b1e3240 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/abricate/tests/main.nf.test.snap b/workflows/bactopia-tools/abricate/tests/main.nf.test.snap index 9d028293a..8de906807 100644 --- a/workflows/bactopia-tools/abricate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/abricate/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-04-29T11:21:24.857027075", + "timestamp": "2026-07-28T17:09:22.296208527", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index d624b2859..32da58938 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap index b50b57dbf..ebd9b6c91 100644 --- a/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap @@ -47,12 +47,12 @@ "GCF_001682305.summary_matches.tsv:md5,2da0b6cb548413f2721a95e55e17e295", "GCF_001682305.summary_partials.tsv:md5,db0255b99826900ecf4616eef7494806", "GCF_001682305.summary_virulence.tsv:md5,439b76b76818cbe8ec06bc82bd2711fe", - "versions.yml:md5,aa30fa16abc1d1a9baefd6defd920a32", + "versions.yml:md5,ef1b96216865ffadde25334b59f3361c", "abritamr.tsv:md5,18df68afa95e104c8f418efedd9146cf", "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-04-29T11:22:41.756272676", + "timestamp": "2026-07-28T17:10:43.990646647", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index f87f0a9a3..01cf5b7d1 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap index 029ea2729..8dad73e3a 100644 --- a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap @@ -49,7 +49,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-04-29T11:21:27.682147015", + "timestamp": "2026-07-28T17:09:27.619314191", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -105,7 +105,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-04-29T11:21:51.115735364", + "timestamp": "2026-07-28T17:09:53.05327239", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index d3fa3d0d6..8c37aafab 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap b/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap index b6513c433..b5f2aed7a 100644 --- a/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-04-29T11:22:00.752046724", + "timestamp": "2026-07-28T19:44:56.138334179", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -86,12 +86,12 @@ ], [ "SRR2838702.tsv:md5,376a8991c8eb010ea64c796115fb9b8d", - "versions.yml:md5,d4aac41b9e2c72836a9b2a1dfed2226c", + "versions.yml:md5,9ca3ec85a3c0993ed41a25321fd6d423", "amrfinderplus.tsv:md5,376a8991c8eb010ea64c796115fb9b8d", "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-04-29T11:21:33.198613166", + "timestamp": "2026-07-28T19:44:39.163411903", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index a542b7414..e3f09e7af 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap index 47394c223..d4c261861 100644 --- a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap @@ -65,7 +65,7 @@ "versions.yml:md5,1a4d97856cb563f9b6c84132cd60d481" ] ], - "timestamp": "2026-04-29T11:21:57.975492018", + "timestamp": "2026-07-28T17:10:00.820155818", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 6019eaab8..862e39360 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap index 644275918..2e09ddbd2 100644 --- a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-04-29T11:27:21.862622123", + "timestamp": "2026-07-28T17:15:29.238808001", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -103,7 +103,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-04-29T11:23:54.843530718", + "timestamp": "2026-07-28T17:11:57.531363246", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index f9275250b..0d3a88e25 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/blastn/tests/main.nf.test.snap b/workflows/bactopia-tools/blastn/tests/main.nf.test.snap index cc8430b62..a127d0b0b 100644 --- a/workflows/bactopia-tools/blastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-04-29T11:21:55.226735741", + "timestamp": "2026-07-28T17:09:59.417235299", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-04-29T11:21:33.528060213", + "timestamp": "2026-07-28T17:09:35.218606399", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-04-29T11:22:21.802394026", + "timestamp": "2026-07-28T17:10:27.796423494", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 2c8003e73..2dda66065 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/blastp/tests/main.nf.test.snap b/workflows/bactopia-tools/blastp/tests/main.nf.test.snap index 945b0730a..1c6c2d7db 100644 --- a/workflows/bactopia-tools/blastp/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastp/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-04-29T11:21:36.868171773", + "timestamp": "2026-07-28T17:09:37.937055755", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-04-29T11:21:59.31536322", + "timestamp": "2026-07-28T17:10:00.568416056", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-04-29T11:22:34.423215856", + "timestamp": "2026-07-28T17:10:29.117992766", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 502076a53..9d85f5bfa 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/blastx/tests/main.nf.test.snap b/workflows/bactopia-tools/blastx/tests/main.nf.test.snap index 52e39f45e..550eecfe2 100644 --- a/workflows/bactopia-tools/blastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-04-29T11:22:02.723228807", + "timestamp": "2026-07-28T17:10:03.595510092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-04-29T11:22:34.420589616", + "timestamp": "2026-07-28T17:10:33.46304634", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-04-29T11:21:42.592357708", + "timestamp": "2026-07-28T17:09:41.05404823", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 98e288684..5fa25fef7 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/bracken/tests/main.nf.test.snap b/workflows/bactopia-tools/bracken/tests/main.nf.test.snap index 785dc2ca2..b52df6a0e 100644 --- a/workflows/bactopia-tools/bracken/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/bracken/tests/main.nf.test.snap @@ -56,17 +56,17 @@ "SRR2838702.bracken.abundances.txt:md5,f487d0ca3b1139b5ea9cbad2272ab03e", "SRR2838702.bracken.adjusted.abundances.txt:md5,9d34ce09aac2ebb8afb257e86581ada9", "SRR2838702.bracken.classification.txt:md5,92291be35925612b304a82ad8e42fcea", - "SRR2838702.bracken.report.txt:md5,184d13c4f0d3248a311a0e9105e5561c", + "SRR2838702.bracken.report.txt:md5,a83588a7c0a33f4f869ed6343419e6d2", "SRR2838702.bracken.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9", - "SRR2838702.kraken2.report.txt:md5,dbc13f97657d22326cabf4bd19564174", - "versions.yml:md5,12f0eff32d10516cc48aea7f50e0fe2f", + "SRR2838702.kraken2.report.txt:md5,0d7991cf80613ba55baf774b0f1140e4", + "versions.yml:md5,da7ea25ff95a475d1b17ff1309a447c6", "bracken-adjusted.tsv:md5,9d34ce09aac2ebb8afb257e86581ada9", "bracken-species-abundance.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9", "versions.yml:md5,95656d5394117a5e9ab88c7503bd2e8f", "versions.yml:md5,eac83c8fd922f581ce913311a557ad9d" ] ], - "timestamp": "2026-04-29T11:33:27.491520486", + "timestamp": "2026-07-28T17:20:56.532841613", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -129,17 +129,17 @@ "SRR2838702.bracken.abundances.txt:md5,f487d0ca3b1139b5ea9cbad2272ab03e", "SRR2838702.bracken.adjusted.abundances.txt:md5,9d34ce09aac2ebb8afb257e86581ada9", "SRR2838702.bracken.classification.txt:md5,92291be35925612b304a82ad8e42fcea", - "SRR2838702.bracken.report.txt:md5,184d13c4f0d3248a311a0e9105e5561c", + "SRR2838702.bracken.report.txt:md5,a83588a7c0a33f4f869ed6343419e6d2", "SRR2838702.bracken.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9", - "SRR2838702.kraken2.report.txt:md5,dbc13f97657d22326cabf4bd19564174", - "versions.yml:md5,12f0eff32d10516cc48aea7f50e0fe2f", + "SRR2838702.kraken2.report.txt:md5,0d7991cf80613ba55baf774b0f1140e4", + "versions.yml:md5,da7ea25ff95a475d1b17ff1309a447c6", "bracken-adjusted.tsv:md5,9d34ce09aac2ebb8afb257e86581ada9", "bracken-species-abundance.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9", "versions.yml:md5,95656d5394117a5e9ab88c7503bd2e8f", "versions.yml:md5,eac83c8fd922f581ce913311a557ad9d" ] ], - "timestamp": "2026-04-29T11:27:09.464659358", + "timestamp": "2026-07-28T17:14:26.988781503", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index aebe64002..8a402b347 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap index 234ea0ac9..f0e52003d 100644 --- a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap @@ -66,7 +66,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-04-29T11:23:27.775940628", + "timestamp": "2026-07-28T17:11:24.979774922", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index 67a26c36d..8a1d2c277 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/busco/tests/main.nf.test.snap b/workflows/bactopia-tools/busco/tests/main.nf.test.snap index 0d1350326..f1b854d5f 100644 --- a/workflows/bactopia-tools/busco/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/busco/tests/main.nf.test.snap @@ -280,14 +280,14 @@ ], [ "SRR2838702-summary.txt:md5,d1cbbfb9ab7dee0204bfa26f3b982620", - "versions.yml:md5,84a39022a8e62bb5b3eb9c860e79d49f", - "full_table.tsv:md5,395616b19c70bb4ff67982cfc4c32511", - "missing_busco_list.tsv:md5,05d02e7e8108d122094d4f90d5dc624b", + "versions.yml:md5,bfe8448c1dd05af49ff6b67f38a9db01", + "full_table.tsv:md5,3b9475a17a9dbfb5b605817bafd464f7", + "missing_busco_list.tsv:md5,e7b37790235c44f6491ed71a98e8e24d", "busco-bacteria_odb10.tsv:md5,d1cbbfb9ab7dee0204bfa26f3b982620", "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-04-29T11:22:08.887451241", + "timestamp": "2026-07-28T17:10:11.725007797", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index ba72bd69b..ae061002c 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/checkm/tests/main.nf.test.snap b/workflows/bactopia-tools/checkm/tests/main.nf.test.snap index 6bbea94a0..8530194e6 100644 --- a/workflows/bactopia-tools/checkm/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/checkm/tests/main.nf.test.snap @@ -91,7 +91,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-04-29T11:23:57.599966838", + "timestamp": "2026-07-28T17:12:03.82480051", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 5c0dec559..0ab63dadb 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap b/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap index 431b2e828..986ababbc 100644 --- a/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-04-29T11:25:59.277809912", + "timestamp": "2026-07-28T17:14:03.76689449", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index 84a35d6ed..60b270af7 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap index 009e3d545..9f1bace01 100644 --- a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-04-29T11:22:20.687508128", + "timestamp": "2026-07-28T17:10:27.878994436", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 7a1617211..9369f434b 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap index 85af8342c..18dd35eb6 100644 --- a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap @@ -70,7 +70,7 @@ "versions.yml:md5,cb06109c537fb7ff30a68b0a1197889d" ] ], - "timestamp": "2026-04-29T11:22:23.942332991", + "timestamp": "2026-07-28T17:10:35.918111152", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index 8fab9475d..be929677a 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap index cccdda070..fbf3090c7 100644 --- a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-04-29T11:22:23.864434", + "timestamp": "2026-07-28T17:10:28.709123296", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index de3d39935..85d535e8b 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap index 5185a8cba..2107ac112 100644 --- a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap @@ -26,10 +26,10 @@ "bactopia-runs/eggnog/nf-reports/eggnog-timeline.html" ], [ - "versions.yml:md5,1b179e895ab51b7321ae747976b92b31" + "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" ] ], - "timestamp": "2026-04-29T11:27:15.558730769", + "timestamp": "2026-07-28T17:15:30.347312097", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index dc4b791d9..3d569c6d6 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap index 5dfae657b..26e5022cc 100644 --- a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-04-29T11:21:59.378233187", + "timestamp": "2026-07-28T17:10:08.616467306", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-04-29T11:22:34.381814729", + "timestamp": "2026-07-28T17:10:38.932643181", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index ecbca2b94..65557a51f 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap index b448de92a..82cf44096 100644 --- a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap @@ -38,7 +38,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-27T13:08:38.973757707", + "timestamp": "2026-07-28T17:11:17.785171064", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-04-29T11:22:34.677999189", + "timestamp": "2026-07-28T17:10:38.958691222", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-04-29T11:22:00.063746589", + "timestamp": "2026-07-28T17:10:08.854942179", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index cf60cdb01..54571dae7 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap index fc9d551cf..338f3e2af 100644 --- a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-04-29T11:22:12.28188556", + "timestamp": "2026-07-28T17:10:14.160012766", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index f905d9462..765cf3f79 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap index ce806cf42..be33cd3c8 100644 --- a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap @@ -57,7 +57,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-04-29T11:22:18.38582236", + "timestamp": "2026-07-28T17:10:27.912243816", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index d20c34106..c7fc2b9a1 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap index 6985f92f9..675dc1528 100644 --- a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-04-29T11:22:29.075791227", + "timestamp": "2026-07-28T17:10:39.152280841", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index c46593d5a..ca65b727c 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap index 975710333..986416e75 100644 --- a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap @@ -43,11 +43,11 @@ "bactopia-runs/gtdb/nf-reports/gtdb-timeline.html" ], [ - "versions.yml:md5,738ac1f744a77df263f3b25b97a2748d", + "versions.yml:md5,07e1a7fe67e8f4acb512d2f15e50f6c3", "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-04-29T11:26:52.98395842", + "timestamp": "2026-07-28T17:15:04.781787076", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index 5f461769b..c405c2646 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap index c1c3df910..e023c3bd5 100644 --- a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap @@ -61,7 +61,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-04-29T11:22:50.299948987", + "timestamp": "2026-07-28T17:11:07.695051593", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index 2df6bb4da..001f157ae 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap index 4d27f257f..2234a836a 100644 --- a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-04-29T11:22:34.484981045", + "timestamp": "2026-07-28T17:10:45.440012805", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 2f9ec1016..69efa8446 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap index 8089ce537..958df9149 100644 --- a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap @@ -1068,7 +1068,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-04-29T11:23:32.385928325", + "timestamp": "2026-07-28T17:11:43.593358144", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index 7e1390d2e..03cf8bdbf 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap index bca502e0d..d463d6cb6 100644 --- a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-04-29T11:23:18.812152838", + "timestamp": "2026-07-28T17:11:29.984572514", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index e7d85b184..04439a30c 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap index 1b9fac9f9..e733d9a0c 100644 --- a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap @@ -24,11 +24,11 @@ "bactopia-runs/kraken2/nf-reports/kraken2-timeline.html" ], [ - "SRR2838702.kraken2.report.txt:md5,dbc13f97657d22326cabf4bd19564174", - "versions.yml:md5,64abaf13d756f2c9443d3b814985e107" + "SRR2838702.kraken2.report.txt:md5,0d7991cf80613ba55baf774b0f1140e4", + "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-04-29T11:27:56.470480451", + "timestamp": "2026-07-28T17:14:20.333481913", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -60,10 +60,10 @@ ], [ "SRR2838702.kraken2.report.txt:md5,055b6535f05d0342e7926ca9603340bf", - "versions.yml:md5,64abaf13d756f2c9443d3b814985e107" + "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-04-29T11:28:24.885961361", + "timestamp": "2026-07-28T17:15:00.893027942", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 7c384f704..44b07df73 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap index f8d5c9f67..8527d964a 100644 --- a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-04-29T11:22:59.111645445", + "timestamp": "2026-07-28T17:11:29.082997324", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index 02cd2040c..700af26e3 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap index e7c7c3131..e4a210acb 100644 --- a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-04-29T11:22:58.886763426", + "timestamp": "2026-07-28T17:11:31.456913119", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index ff07b93e4..161a735fb 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap index 48bafc325..722b48841 100644 --- a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap @@ -43,7 +43,7 @@ "mashdist.tsv:md5,630500729ddf987a8f487cd409d0afce" ] ], - "timestamp": "2026-04-29T11:23:16.331571212", + "timestamp": "2026-07-28T17:11:35.231047777", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index c6808120e..b62814547 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap index 4db668630..1866ccc0f 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "mashtree.dnd:md5,2b2d08b0bf16e25717f5db0eca6eba6b" ] ], - "timestamp": "2026-04-29T11:23:17.010786547", + "timestamp": "2026-07-28T17:11:37.241906731", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "mashtree.dnd:md5,02f89fd1a5f4a3a92df0b016061f67dd" ] ], - "timestamp": "2026-07-27T12:38:27.600224868", + "timestamp": "2026-07-28T17:12:06.423579656", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 26af1ef1c..334d25af3 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap index edfed7480..e6148e902 100644 --- a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "mcroni.tsv:md5,c5459d2965dfafe22f173023d0c35610" ] ], - "timestamp": "2026-04-29T11:23:26.898150496", + "timestamp": "2026-07-28T17:11:44.024513745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index 9be7071d8..1ffcfbe58 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap index 4c8a20213..92b4b2ec0 100644 --- a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "meningotype.tsv:md5,cdf1cbd9f28a9ce2138f072c6d0ab391" ] ], - "timestamp": "2026-04-29T11:23:30.358881973", + "timestamp": "2026-07-28T17:11:44.713911402", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index 15f0587b9..a8acf679d 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap index 0699a75c6..f97f190ca 100644 --- a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap @@ -386,7 +386,7 @@ ] ], - "timestamp": "2026-05-05T13:26:46.601147931", + "timestamp": "2026-07-28T17:13:34.747448959", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -973,7 +973,7 @@ ] ], - "timestamp": "2026-05-05T13:27:58.035964435", + "timestamp": "2026-07-28T17:15:25.362968386", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index fbb77c843..85006c2ab 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/midas/tests/main.nf.test.snap b/workflows/bactopia-tools/midas/tests/main.nf.test.snap index 43db30361..9d36f4277 100644 --- a/workflows/bactopia-tools/midas/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/midas/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-04-29T11:24:15.40797744", + "timestamp": "2026-07-28T17:12:30.355218637", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -99,7 +99,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-04-29T11:25:21.435687768", + "timestamp": "2026-07-28T17:13:34.746758901", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index 3792ff1fc..c2e7353c6 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap index ede6ba26a..54882f160 100644 --- a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap @@ -37,12 +37,12 @@ ], [ "GCF_000017085.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6", - "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee", + "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e", "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc", "mlst.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6" ] ], - "timestamp": "2026-04-29T11:23:42.139593519", + "timestamp": "2026-07-28T17:11:59.576599362", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index 12cda34b1..f91c8d0a1 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap index ac8b9c171..0c0419735 100644 --- a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "mobsuite.tsv:md5,951dbd706ab78c4d00aa28735ab34e87" ] ], - "timestamp": "2026-04-29T11:24:21.232121928", + "timestamp": "2026-07-28T17:12:34.151817352", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index 60e85dc52..8564e5008 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap index 1a5886383..7c089150d 100644 --- a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap @@ -41,7 +41,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-04-29T11:23:46.472023379", + "timestamp": "2026-07-28T17:11:58.029504474", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index fa4dfd990..4de56a598 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap index f094807e5..523f5286c 100644 --- a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap @@ -37,12 +37,12 @@ ], [ "GCF_001047255.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219", - "versions.yml:md5,dcc7b71de52c4fe65e10147be956aa05", + "versions.yml:md5,67ed215f25e8d088f830fb7d63ab9df5", "versions.yml:md5,9dbc0e8b7902e955ec10c94c11074f06", "ngmaster.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219" ] ], - "timestamp": "2026-04-29T11:23:59.895408082", + "timestamp": "2026-07-28T17:12:06.096077734", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index ef21927f6..bc56107f3 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/pangenome/tests/.nftignore b/workflows/bactopia-tools/pangenome/tests/.nftignore index 7b289fb58..d9d90783e 100644 --- a/workflows/bactopia-tools/pangenome/tests/.nftignore +++ b/workflows/bactopia-tools/pangenome/tests/.nftignore @@ -8,3 +8,4 @@ bactopia-runs/**/nf-reports/*.{dot,html} **/gene_presence_absence.csv **/gene_presence_absence_roary.csv **/pan_sequences.representative.fasta* +**/alignment_resume_state.json diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap index e0b224b6a..73969655c 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap @@ -132,15 +132,15 @@ ], [ "versions.yml:md5,70f831abce5d4f7f4ad4177a0ad339cc", - "versions.yml:md5,2998af40c25f65e228af5938ff93448e", - "versions.yml:md5,e01256842798c2b435032141a36e34a4", + "versions.yml:md5,a8001abd80c493ec7ae6d20498bcd5bf", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", "versions.yml:md5,15428b6f6c4a355e8944a4f92f0390c7", "versions.yml:md5,36d9b366d4941f258a248bf7a31aecc7", "versions.yml:md5,77f64a20eeab9152a61953ec5203b926", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:30:18.404904236", + "timestamp": "2026-07-28T20:08:29.948976259", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -307,14 +307,14 @@ ], [ "versions.yml:md5,70f831abce5d4f7f4ad4177a0ad339cc", - "versions.yml:md5,2998af40c25f65e228af5938ff93448e", - "versions.yml:md5,e01256842798c2b435032141a36e34a4", + "versions.yml:md5,a8001abd80c493ec7ae6d20498bcd5bf", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", "versions.yml:md5,826c93ad04efd1f51b1e1a009d5c0ba7", "versions.yml:md5,77f64a20eeab9152a61953ec5203b926", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:27:43.40448099", + "timestamp": "2026-07-28T20:06:33.807080285", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -440,14 +440,14 @@ ], [ "versions.yml:md5,70f831abce5d4f7f4ad4177a0ad339cc", - "versions.yml:md5,2998af40c25f65e228af5938ff93448e", - "versions.yml:md5,e01256842798c2b435032141a36e34a4", + "versions.yml:md5,a8001abd80c493ec7ae6d20498bcd5bf", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", "versions.yml:md5,15428b6f6c4a355e8944a4f92f0390c7", "versions.yml:md5,77f64a20eeab9152a61953ec5203b926", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:28:59.354294099", + "timestamp": "2026-07-28T20:07:31.819117432", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -524,6 +524,7 @@ "bactopia-runs/pangenome/panaroo.filtered.aln.gz", "bactopia-runs/pangenome/panaroo/aligned_gene_sequences", "bactopia-runs/pangenome/panaroo/alignment_entropy.csv", + "bactopia-runs/pangenome/panaroo/alignment_resume_state.json", "bactopia-runs/pangenome/panaroo/combined_DNA_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_cdhit_out.txt", @@ -571,14 +572,14 @@ ], [ "versions.yml:md5,70f831abce5d4f7f4ad4177a0ad339cc", - "versions.yml:md5,2998af40c25f65e228af5938ff93448e", - "versions.yml:md5,e01256842798c2b435032141a36e34a4", - "versions.yml:md5,5514295ba35a95ebb8417acd05766159", + "versions.yml:md5,a8001abd80c493ec7ae6d20498bcd5bf", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", + "versions.yml:md5,709f42df442c9f6cc5132ad147bd334e", "versions.yml:md5,77f64a20eeab9152a61953ec5203b926", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:25:18.043114573", + "timestamp": "2026-07-28T20:03:47.313952314", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -620,6 +621,7 @@ "bactopia-runs/pangenome/panaroo.filtered.aln.gz", "bactopia-runs/pangenome/panaroo/aligned_gene_sequences", "bactopia-runs/pangenome/panaroo/alignment_entropy.csv", + "bactopia-runs/pangenome/panaroo/alignment_resume_state.json", "bactopia-runs/pangenome/panaroo/combined_DNA_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_cdhit_out.txt", @@ -656,12 +658,12 @@ "bactopia-runs/pangenome/snpdists/logs/versions.yml" ], [ - "versions.yml:md5,e01256842798c2b435032141a36e34a4", - "versions.yml:md5,5514295ba35a95ebb8417acd05766159", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", + "versions.yml:md5,709f42df442c9f6cc5132ad147bd334e", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-04-29T11:26:18.912862645", + "timestamp": "2026-07-28T20:04:27.323618465", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -703,6 +705,7 @@ "bactopia-runs/pangenome/panaroo.filtered.aln.gz", "bactopia-runs/pangenome/panaroo/aligned_gene_sequences", "bactopia-runs/pangenome/panaroo/alignment_entropy.csv", + "bactopia-runs/pangenome/panaroo/alignment_resume_state.json", "bactopia-runs/pangenome/panaroo/combined_DNA_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_CDS.fasta.gz", "bactopia-runs/pangenome/panaroo/combined_protein_cdhit_out.txt", @@ -739,12 +742,12 @@ "bactopia-runs/pangenome/snpdists/logs/versions.yml" ], [ - "versions.yml:md5,e01256842798c2b435032141a36e34a4", - "versions.yml:md5,5514295ba35a95ebb8417acd05766159", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", + "versions.yml:md5,709f42df442c9f6cc5132ad147bd334e", "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-27T13:10:28.183576616", + "timestamp": "2026-07-28T20:05:19.973058681", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index e025970b1..c0a65596c 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap index b18fcc381..f6a3f66d5 100644 --- a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "pasty.tsv:md5,3f0b647b733d1c01212c1f475527aef4" ] ], - "timestamp": "2026-04-29T11:23:50.707543844", + "timestamp": "2026-07-28T17:12:08.300371346", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index e0c20ca3d..1cea8a4a3 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap index 8db1e4eb5..c7cd5dc47 100644 --- a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "pbptyper.tsv:md5,34edc1f9346b74b74ef4446d270e6d57" ] ], - "timestamp": "2026-04-29T11:24:22.709047733", + "timestamp": "2026-07-28T17:12:43.010445622", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index e1efd97b1..fdbb993f5 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap index baf594481..8a4cee6a2 100644 --- a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap @@ -55,12 +55,12 @@ "bactopia-runs/phispy/nf-reports/phispy-timeline.html" ], [ - "versions.yml:md5,6487fa342391eda548b492a099ee91ed", - "versions.yml:md5,6487fa342391eda548b492a099ee91ed", + "versions.yml:md5,5e1425957e8a8025744f6a4d4dbb24cf", + "versions.yml:md5,5e1425957e8a8025744f6a4d4dbb24cf", "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-04-29T11:24:39.747961501", + "timestamp": "2026-07-28T17:12:55.882689995", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index 9c1bca127..d9fac182a 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap index 792000550..1fc2ebf9e 100644 --- a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-04-29T11:23:57.039800861", + "timestamp": "2026-07-28T17:12:17.278174521", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index 3847fbbdb..41bfa3d3e 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap index 98f83fd43..e75ba67c5 100644 --- a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-04-29T11:23:55.183229181", + "timestamp": "2026-07-28T17:12:19.823973883", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index 4d2a78469..36d42cb5d 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap index 781e5dca1..30941ef56 100644 --- a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-04-29T11:24:02.431203572", + "timestamp": "2026-07-28T17:12:30.648349748", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 68a7f4582..1d6d3526f 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/quast/tests/main.nf.test.snap b/workflows/bactopia-tools/quast/tests/main.nf.test.snap index ce291c5ff..673f07bbc 100644 --- a/workflows/bactopia-tools/quast/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/quast/tests/main.nf.test.snap @@ -69,7 +69,7 @@ "quast.tsv:md5,a02f798379d9982810a198ec9b389079" ] ], - "timestamp": "2026-04-29T11:24:09.935936083", + "timestamp": "2026-07-28T17:12:37.761771394", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index f4aa4d367..8a5081e4d 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/rgi/nextflow_schema.json b/workflows/bactopia-tools/rgi/nextflow_schema.json index fe6c717e0..aee006e32 100644 --- a/workflows/bactopia-tools/rgi/nextflow_schema.json +++ b/workflows/bactopia-tools/rgi/nextflow_schema.json @@ -62,10 +62,10 @@ "fa_icon": "fas fa-toggle-on", "hidden": true }, - "rgi_exclude_nudge": { + "rgi_include_nudge": { "type": "boolean", "default": false, - "description": "Exclude hits nudged from loose to strict hits", + "description": "Include hits nudged from loose to strict hits", "fa_icon": "fas fa-toggle-on", "hidden": true }, diff --git a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap index e55683b9a..1d1a234ef 100644 --- a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap @@ -65,18 +65,18 @@ "bactopia-runs/rgi/rgi-heatmap/rgi-2.png" ], [ - "GCA_000027305.json:md5,e50aca7b17a080c5be68b1322809a968", - "GCA_000027305.tsv:md5,4207abf2986a420c0fb15b33e77144a6", - "versions.yml:md5,4a19310417d04abb9e1eeec05629f944", - "GCF_900478275.json:md5,6c403fb8e2f24b7c88be27ba5a30ca70", - "GCF_900478275.tsv:md5,9d7754551163e020beed52a8bc14ce83", - "versions.yml:md5,4a19310417d04abb9e1eeec05629f944", + "GCA_000027305.json:md5,d0227a9c5754923eb9b4659e216bf027", + "GCA_000027305.tsv:md5,9af9b3e370a908d6b86a21c2cecad254", + "versions.yml:md5,6a43ca3ba925940f762a035f862fc657", + "GCF_900478275.json:md5,74b89120ae465892ef013014e44a8ab4", + "GCF_900478275.tsv:md5,9dd0afe6946da9c6608e775f954813a1", + "versions.yml:md5,6a43ca3ba925940f762a035f862fc657", "versions.yml:md5,c1294552ba205b057bd368875a4eac93", - "rgi.tsv:md5,6dabb1f8c3cab56929ecab6236f6fa67", - "versions.yml:md5,84fa922dc8ecb987b4ee03caffd09c32" + "rgi.tsv:md5,29bd05873135b291069b7325cfee4561", + "versions.yml:md5,69941ec700f55e09c1a930ed36f54b0c" ] ], - "timestamp": "2026-04-29T11:25:13.539158196", + "timestamp": "2026-07-28T18:33:45.287947145", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index bf0ea381f..0bae60834 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap index 8364f7598..dd84b7f4a 100644 --- a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap @@ -50,7 +50,7 @@ "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" ] ], - "timestamp": "2026-04-29T11:24:41.576473233", + "timestamp": "2026-07-28T17:13:13.950341218", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -107,7 +107,7 @@ "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" ] ], - "timestamp": "2026-04-29T11:24:09.888484492", + "timestamp": "2026-07-28T17:12:37.38061554", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index 330cc209e..88c45dd7a 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap index 95304432e..93d281edc 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "scrubber.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d" ] ], - "timestamp": "2026-05-06T15:45:32.588701069", + "timestamp": "2026-07-28T17:12:47.592328778", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -96,7 +96,7 @@ "scrubber.tsv:md5,e957775ff85716621f5fdd536de5b417" ] ], - "timestamp": "2026-05-06T15:48:31.038388568", + "timestamp": "2026-07-28T17:17:02.76227411", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "scrubber.tsv:md5,9554a4a6929bbfd485e28acd4a716772" ] ], - "timestamp": "2026-05-06T15:49:11.183710425", + "timestamp": "2026-07-28T17:17:57.711891391", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index b577cfe5b..54af2cc47 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap index f9e062309..f8913cc21 100644 --- a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-04-29T11:24:08.916545738", + "timestamp": "2026-07-28T17:12:37.848465503", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index a461f7ec3..30d904d5c 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap index d3a69acfe..ea6cb3475 100644 --- a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "seroba.tsv:md5,8c20690cc5ca0fd77228c830001e0b86" ] ], - "timestamp": "2026-04-29T11:24:53.825951358", + "timestamp": "2026-07-28T17:13:10.815719428", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index c23c6564b..321107a3f 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap index f4fd3f5b4..92ce774b8 100644 --- a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "shigapass.tsv:md5,9982dbc252423a0507b7c397f66164f2" ] ], - "timestamp": "2026-04-29T11:24:28.361228337", + "timestamp": "2026-07-28T17:12:49.478347629", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 64694332c..8470666fe 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap index 0041599d1..73f4c3dd5 100644 --- a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap @@ -78,7 +78,7 @@ "shigatyper.tsv:md5,6041948e454daeabef20a6f725047dca" ] ], - "timestamp": "2026-04-29T11:24:23.343691466", + "timestamp": "2026-07-28T17:12:44.466999633", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 0040ec10f..1af978427 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap index 8b041116f..dc5775a46 100644 --- a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "shigeifinder.tsv:md5,25be6cf1161e59d9a4eab8db8f9b9ebb" ] ], - "timestamp": "2026-04-29T11:24:21.227838831", + "timestamp": "2026-07-28T17:12:47.76154099", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index e6461b336..26cf199a3 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap index efe65d055..b59215e7b 100644 --- a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-04-29T11:25:02.198301037", + "timestamp": "2026-07-28T17:13:17.569264055", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 61d6febc1..4aef670ab 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap index 81f59e17a..c1d8dbb15 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap @@ -316,7 +316,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:25:28.294717847", + "timestamp": "2026-07-28T17:13:59.293503099", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -639,7 +639,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:26:29.494050082", + "timestamp": "2026-07-28T17:15:06.651723264", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -944,12 +944,12 @@ "SRR2838702_2.tab:md5,0cc5a62da2cd9c7c1aefa5446a7bfb4e", "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30", "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1", - "versions.yml:md5,e01256842798c2b435032141a36e34a4", + "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f", "versions.yml:md5,27ed685c7bc2cfe49934a9c45b1a2735", "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:27:24.977637504", + "timestamp": "2026-07-28T17:16:01.437051468", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1238,7 +1238,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:29:03.688696937", + "timestamp": "2026-07-28T17:17:39.155144399", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1561,7 +1561,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-04-29T11:28:20.204763447", + "timestamp": "2026-07-28T17:16:56.477900542", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1850,7 +1850,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-27T13:04:19.490489215", + "timestamp": "2026-07-28T17:18:27.063251165", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index 519c421f8..fcb3ffe9a 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap index 049610333..28ad5204b 100644 --- a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-04-29T11:25:16.346934706", + "timestamp": "2026-07-28T17:13:43.063262582", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-04-29T11:24:33.661292996", + "timestamp": "2026-07-28T17:13:14.025244723", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 9358ac1da..878c6f928 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap index 9054adb8c..940637fff 100644 --- a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ssuissero.tsv:md5,b1312d3041a6543154be554d5ec3b0b9" ] ], - "timestamp": "2026-04-29T11:24:32.770143641", + "timestamp": "2026-07-28T17:13:10.156993552", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index 83b4c7330..2b89d97a2 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap index 2ea85b322..be845985f 100644 --- a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap @@ -36,13 +36,13 @@ "bactopia-runs/staphscan/nf-reports/staphscan-timeline.html" ], [ - "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", - "versions.yml:md5,21366a5b932268b20a58c129bf66d90b", + "GCF_000017085.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e", + "versions.yml:md5,794f66edfdb0127b7c9b08a1bb6d3231", "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b", - "staphscan.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb" + "staphscan.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e" ] ], - "timestamp": "2026-05-05T12:05:58.045626143", + "timestamp": "2026-07-28T17:13:29.892080708", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index c30928f5c..0d698fde4 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap index 3c29ccbe1..0169e3493 100644 --- a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap @@ -120,8 +120,8 @@ "versions.yml:md5,4d90b86147c4eb115fc93edc4fa484b8", "GCF_000017085.tsv:md5,6afe7a90c591e32107d86c0e81029f54", "versions.yml:md5,32d57feabda90e9fe6e0aeb96e5d2352", - "GCF_000017085.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb", - "versions.yml:md5,9048a4caf373fcb35bb1f990c90ddcf0", + "GCF_000017085.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e", + "versions.yml:md5,70a740425288fd57db5b227c8a1b3723", "agrvate.tsv:md5,6acd3d01fc9d867f32435265331ff7b2", "versions.yml:md5,d203f21af354f31f3d144e58af47cff3", "versions.yml:md5,35f4a9f839e9fd13b2afb63fecea88b4", @@ -129,10 +129,10 @@ "versions.yml:md5,c707d4291d068c2b150937480568d0b0", "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975", "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54", - "staphscan.tsv:md5,c8d77f01e4a86869bc4ae82141b500cb" + "staphscan.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e" ] ], - "timestamp": "2026-05-05T13:24:58.587861386", + "timestamp": "2026-07-28T17:13:34.568119151", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index b2d596299..2a5742948 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap index 5b863bda3..7883e80f5 100644 --- a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap @@ -72,7 +72,7 @@ "stecfinder.tsv:md5,d2b6d9a9ab37d918c58b4e8272e6055d" ] ], - "timestamp": "2026-04-29T11:24:45.875265794", + "timestamp": "2026-07-28T17:13:23.504001293", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stxtyper/nextflow.config b/workflows/bactopia-tools/stxtyper/nextflow.config index fa62e8f45..acbefdc82 100644 --- a/workflows/bactopia-tools/stxtyper/nextflow.config +++ b/workflows/bactopia-tools/stxtyper/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap index dcd0ab339..6236d0091 100644 --- a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "stxtyper.tsv:md5,99f9ffe60fe519d684ee7943641022d2" ] ], - "timestamp": "2026-05-21T13:59:39.436267755", + "timestamp": "2026-07-28T17:13:29.110420034", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 41dad8235..846ab8b00 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap index 6824afd8d..024a25769 100644 --- a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "sylph.tsv:md5,beb99cbcea3c9c0a90329ae09ee957f3" ] ], - "timestamp": "2026-04-29T11:25:40.903377434", + "timestamp": "2026-07-28T17:14:10.754008226", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index 1b04e2a15..83a5a08dd 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap index 5e6b9cb3a..b0054cdb3 100644 --- a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-04-29T11:25:02.939135967", + "timestamp": "2026-07-28T17:13:27.965097802", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-04-29T11:25:25.437151337", + "timestamp": "2026-07-28T17:13:50.244084431", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 11ab0ea1a..25f625fcc 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap index ea1f4ea42..be5d51878 100644 --- a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-04-29T11:25:02.164029782", + "timestamp": "2026-07-28T17:13:34.466516621", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-04-29T11:25:44.140544124", + "timestamp": "2026-07-28T17:14:14.607756685", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "tblastx.tsv:md5,4efa1d2d8633246603e06df64e559c4c" ] ], - "timestamp": "2026-04-29T11:25:25.520504118", + "timestamp": "2026-07-28T17:13:56.338698945", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 91473f848..906ca4513 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap index 2ecaf81e5..9ddb63927 100644 --- a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-04-29T11:25:39.710272209", + "timestamp": "2026-07-28T17:14:01.47336561", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index a86378106..6f9be3887 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -19,7 +19,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap index d597d693f..cfd48de17 100644 --- a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-05-06T09:00:06.520660486", + "timestamp": "2026-07-28T17:17:36.679585092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index cf8325fbf..9ef6f6c84 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/cleanyerreads/nextflow_schema.json b/workflows/cleanyerreads/nextflow_schema.json index ca3ffffc8..0b45d78bd 100644 --- a/workflows/cleanyerreads/nextflow_schema.json +++ b/workflows/cleanyerreads/nextflow_schema.json @@ -138,12 +138,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-toggle-on", - "hidden": true } } }, diff --git a/workflows/cleanyerreads/tests/main.nf.test.snap b/workflows/cleanyerreads/tests/main.nf.test.snap index 2ea5ec100..9a95b2638 100644 --- a/workflows/cleanyerreads/tests/main.nf.test.snap +++ b/workflows/cleanyerreads/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bactopia-runs/cleanyerreads/nf-reports/cleanyerreads-timeline.html" ], [ - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", "versions.yml:md5,74fd99ec158fe3e666d2ba871c809827", "versions.yml:md5,61924107a406c136f55c445d470721f7", "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-05-06T14:41:16.282494509", + "timestamp": "2026-07-28T17:15:58.316832451", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -158,12 +158,12 @@ "bactopia-runs/cleanyerreads/nf-reports/cleanyerreads-timeline.html" ], [ - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", "versions.yml:md5,61924107a406c136f55c445d470721f7" ] ], - "timestamp": "2026-05-06T14:40:34.994298384", + "timestamp": "2026-07-28T17:14:35.365789194", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index d8b32a034..3a934ad53 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index 46d3e6623..711c74d2f 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -467,12 +467,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-toggle-on", - "hidden": true } } }, diff --git a/workflows/staphopia/tests/main.nf.test.snap b/workflows/staphopia/tests/main.nf.test.snap index 346c80ece..f67f5e8ee 100644 --- a/workflows/staphopia/tests/main.nf.test.snap +++ b/workflows/staphopia/tests/main.nf.test.snap @@ -270,15 +270,15 @@ [ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e", "versions.yml:md5,5d00225a5ad24de728e651fdd0d7d1e3", - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", "versions.yml:md5,e46de3078794860a978e2dd0b390c27c", "versions.yml:md5,c0b16a8b5ea1a55c72f38545beffb659", - "versions.yml:md5,d4aac41b9e2c72836a9b2a1dfed2226c", - "versions.yml:md5,feb26d507cd4d8f25033d4950ba463ee", + "versions.yml:md5,9ca3ec85a3c0993ed41a25321fd6d423", + "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e", "versions.yml:md5,4d90b86147c4eb115fc93edc4fa484b8", "versions.yml:md5,32d57feabda90e9fe6e0aeb96e5d2352", - "versions.yml:md5,9048a4caf373fcb35bb1f990c90ddcf0", + "versions.yml:md5,70a740425288fd57db5b227c8a1b3723", "versions.yml:md5,d203f21af354f31f3d144e58af47cff3", "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6", "versions.yml:md5,1913efda4329af168df4ab88555dbeb4", @@ -289,7 +289,7 @@ "versions.yml:md5,c707d4291d068c2b150937480568d0b0" ] ], - "timestamp": "2026-05-05T13:34:09.075806826", + "timestamp": "2026-07-28T17:18:23.171217804", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index d2da6c557..637952352 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -5,7 +5,7 @@ manifest { homePage = 'https://github.com/bactopia/bactopia' description = 'An extensive workflow for processing sequencing of bacterial genomes.' mainScript = 'main.nf' - version = '4.0.1' + version = '4.1.0' nextflowVersion = '>=26.04.0' } @@ -18,7 +18,7 @@ params { } // Version -params.bactopia_version = '4.0.1' +params.bactopia_version = '4.1.0' manifest.version = "${params.bactopia_version}" // Includes diff --git a/workflows/teton/nextflow_schema.json b/workflows/teton/nextflow_schema.json index 3cd95e952..4b9af5a0c 100644 --- a/workflows/teton/nextflow_schema.json +++ b/workflows/teton/nextflow_schema.json @@ -138,12 +138,6 @@ "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true - }, - "no_cache": { - "type": "boolean", - "description": "Skip caching the assembly summary file from ncbi-genome-download", - "fa_icon": "fas fa-toggle-on", - "hidden": true } } }, diff --git a/workflows/teton/tests/main.nf.test.snap b/workflows/teton/tests/main.nf.test.snap index 383e97382..10e331af5 100644 --- a/workflows/teton/tests/main.nf.test.snap +++ b/workflows/teton/tests/main.nf.test.snap @@ -166,7 +166,7 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", "versions.yml:md5,7d27773f1e349726172140b0c615a73b", "versions.yml:md5,b567c9f0928098cfc68f12308a3372f0", @@ -181,7 +181,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-05-06T15:20:19.345378436", + "timestamp": "2026-07-28T17:18:44.389172726", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -353,7 +353,7 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", "versions.yml:md5,7d27773f1e349726172140b0c615a73b", "versions.yml:md5,5ccb1a29e9b0dfff5b4a46a6e73facf3", @@ -368,7 +368,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-05-06T15:30:11.50655874", + "timestamp": "2026-07-28T17:28:45.981302767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -540,7 +540,7 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,cd4830d4b299d4776ea68dce5a1c9e73", + "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", "versions.yml:md5,7d27773f1e349726172140b0c615a73b", "versions.yml:md5,14feb3b47ba66dc6b247bdd7debcc18c", @@ -555,7 +555,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-05-06T15:26:01.705868003", + "timestamp": "2026-07-28T17:23:34.852640834", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 0d607269338fefd444052bd6196a6e940114a015 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 29 Jul 2026 10:58:11 -0600 Subject: [PATCH 27/43] update test snapshots --- CHANGELOG.md | 8 +- catalog.json | 7 +- data/conda/meta.yaml | 2 +- modules/abricate/run/tests/main.nf.test.snap | 2 +- .../abricate/summary/tests/main.nf.test.snap | 2 +- modules/abritamr/run/tests/main.nf.test.snap | 4 +- modules/agrvate/tests/main.nf.test.snap | 4 +- .../amrfinderplus/run/tests/main.nf.test.snap | 4 +- modules/ariba/run/tests/main.nf.test.snap | 2 +- .../assembler/tests/main.nf.test.snap | 16 +- .../bactopia/gather/tests/main.nf.test.snap | 16 +- modules/bactopia/qc/tests/main.nf.test.snap | 10 +- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- .../bactopia/teton/tests/main.nf.test.snap | 4 +- modules/bakta/run/tests/main.nf.test.snap | 4 +- modules/blast/blastn/tests/main.nf.test.snap | 2 +- modules/blast/blastp/tests/main.nf.test.snap | 2 +- modules/blast/blastx/tests/main.nf.test.snap | 2 +- modules/blast/tblastn/tests/main.nf.test.snap | 2 +- modules/blast/tblastx/tests/main.nf.test.snap | 2 +- modules/bracken/tests/main.nf.test.snap | 4 +- modules/btyper3/tests/main.nf.test.snap | 4 +- modules/busco/tests/main.nf.test.snap | 4 +- .../checkm/lineagewf/tests/main.nf.test.snap | 4 +- .../checkm2/predict/tests/main.nf.test.snap | 4 +- modules/clermontyping/tests/main.nf.test.snap | 4 +- modules/clonalframeml/tests/main.nf.test.snap | 4 +- modules/csvtk/concat/tests/main.nf.test.snap | 4 +- modules/csvtk/join/tests/main.nf.test.snap | 4 +- modules/deacon/filter/tests/main.nf.test.snap | 6 +- .../defensefinder/run/tests/main.nf.test.snap | 2 +- modules/ectyper/tests/main.nf.test.snap | 4 +- modules/eggnog/mapper/tests/main.nf.test.snap | 4 +- modules/emmtyper/tests/main.nf.test.snap | 6 +- modules/fastani/tests/main.nf.test.snap | 4 +- modules/gamma/tests/main.nf.test.snap | 4 +- modules/genomedl/tests/main.nf.test.snap | 6 +- .../genotyphi/parse/tests/main.nf.test.snap | 2 +- modules/gigatyper/tests/main.nf.test.snap | 2 +- .../gtdbtk/classifywf/tests/main.nf.test.snap | 2 +- modules/gubbins/tests/main.nf.test.snap | 4 +- modules/hicap/tests/main.nf.test.snap | 8 +- modules/hpsuissero/tests/main.nf.test.snap | 4 +- modules/iqtree/tests/main.nf.test.snap | 4 +- modules/ismapper/tests/main.nf.test.snap | 2 +- modules/kleborate/tests/main.nf.test.snap | 2 +- modules/kraken2/tests/main.nf.test.snap | 4 +- modules/legsta/tests/main.nf.test.snap | 2 +- modules/lissero/tests/main.nf.test.snap | 4 +- modules/mash/dist/tests/main.nf.test.snap | 4 +- modules/mashtree/tests/main.nf.test.snap | 2 +- modules/mcroni/tests/main.nf.test.snap | 4 +- modules/meningotype/tests/main.nf.test.snap | 4 +- modules/merlin/dist/tests/main.nf.test.snap | 4 +- modules/midas/species/tests/main.nf.test.snap | 4 +- modules/mlst/tests/main.nf.test.snap | 2 +- .../mobsuite/recon/tests/main.nf.test.snap | 6 +- .../mykrobe/predict/tests/main.nf.test.snap | 2 +- modules/ngmaster/tests/main.nf.test.snap | 4 +- modules/nohuman/run/tests/main.nf.test.snap | 6 +- modules/panaroo/run/tests/main.nf.test.snap | 2 +- modules/pasty/tests/main.nf.test.snap | 2 +- modules/pbptyper/tests/main.nf.test.snap | 2 +- modules/phispy/tests/main.nf.test.snap | 2 +- modules/pirate/tests/main.nf.test.snap | 2 +- modules/plasmidfinder/tests/main.nf.test.snap | 4 +- modules/pneumocat/tests/main.nf.test.snap | 2 +- modules/prokka/tests/main.nf.test.snap | 6 +- modules/quast/tests/main.nf.test.snap | 6 +- modules/rgi/heatmap/tests/main.nf.test.snap | 2 +- modules/rgi/main/module.config | 2 +- modules/rgi/main/tests/main.nf.test.snap | 6 +- modules/roary/tests/main.nf.test.snap | 2 +- modules/sccmec/tests/main.nf.test.snap | 4 +- modules/scoary/tests/main.nf.test.snap | 2 +- modules/seqsero2/tests/main.nf.test.snap | 4 +- modules/seroba/run/tests/main.nf.test.snap | 2 +- modules/shigapass/tests/main.nf.test.snap | 4 +- modules/shigatyper/tests/main.nf.test.snap | 2 +- modules/shigeifinder/tests/main.nf.test.snap | 4 +- modules/sistr/tests/main.nf.test.snap | 4 +- modules/snippy/core/tests/main.nf.test.snap | 2 +- modules/snippy/run/tests/main.nf.test.snap | 4 +- modules/snpdists/tests/main.nf.test.snap | 2 +- modules/spatyper/tests/main.nf.test.snap | 4 +- .../scrub/tests/main.nf.test.snap | 4 +- modules/ssuissero/tests/main.nf.test.snap | 4 +- .../staphopiasccmec/tests/main.nf.test.snap | 4 +- modules/staphscan/tests/main.nf.test.snap | 2 +- modules/stecfinder/tests/main.nf.test.snap | 6 +- modules/stxtyper/tests/main.nf.test.snap | 2 +- modules/sylph/profile/tests/main.nf.test.snap | 4 +- .../collate/tests/main.nf.test.snap | 2 +- .../profile/tests/main.nf.test.snap | 6 +- modules/traitar/run/tests/main.nf.test.snap | 4 +- subworkflows/abricate/tests/main.nf.test.snap | 2 +- subworkflows/abritamr/tests/main.nf.test.snap | 2 +- subworkflows/agrvate/tests/main.nf.test.snap | 2 +- .../amrfinderplus/tests/main.nf.test.snap | 2 +- subworkflows/ariba/tests/main.nf.test.snap | 2 +- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- subworkflows/bakta/tests/main.nf.test.snap | 2 +- subworkflows/blastn/tests/main.nf.test.snap | 2 +- subworkflows/blastp/tests/main.nf.test.snap | 2 +- subworkflows/blastx/tests/main.nf.test.snap | 2 +- subworkflows/btyper3/tests/main.nf.test.snap | 2 +- subworkflows/busco/tests/main.nf.test.snap | 2 +- subworkflows/checkm/tests/main.nf.test.snap | 2 +- subworkflows/checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../clonalframeml/tests/main.nf.test.snap | 2 +- subworkflows/deacon/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- subworkflows/ectyper/tests/main.nf.test.snap | 2 +- subworkflows/eggnog/tests/main.nf.test.snap | 2 +- subworkflows/emmtyper/tests/main.nf.test.snap | 2 +- subworkflows/fastani/tests/main.nf.test.snap | 2 +- subworkflows/gamma/tests/main.nf.test.snap | 2 +- subworkflows/genomedl/tests/main.nf.test.snap | 6 +- .../genotyphi/tests/main.nf.test.snap | 2 +- .../gigatyper/tests/main.nf.test.snap | 2 +- subworkflows/gtdb/tests/main.nf.test.snap | 2 +- subworkflows/gubbins/tests/main.nf.test.snap | 2 +- subworkflows/hicap/tests/main.nf.test.snap | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- subworkflows/iqtree/tests/main.nf.test.snap | 2 +- subworkflows/ismapper/tests/main.nf.test.snap | 2 +- .../kleborate/tests/main.nf.test.snap | 2 +- subworkflows/kraken2/tests/main.nf.test.snap | 2 +- subworkflows/legsta/tests/main.nf.test.snap | 2 +- subworkflows/lissero/tests/main.nf.test.snap | 2 +- subworkflows/mashdist/tests/main.nf.test.snap | 2 +- subworkflows/mashtree/tests/main.nf.test.snap | 2 +- subworkflows/mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../merlindist/tests/main.nf.test.snap | 2 +- subworkflows/midas/tests/main.nf.test.snap | 2 +- subworkflows/mlst/tests/main.nf.test.snap | 2 +- subworkflows/mobsuite/tests/main.nf.test.snap | 2 +- subworkflows/mykrobe/tests/main.nf.test.snap | 2 +- subworkflows/ngmaster/tests/main.nf.test.snap | 2 +- subworkflows/nohuman/tests/main.nf.test.snap | 2 +- subworkflows/panaroo/tests/main.nf.test.snap | 2 +- .../pangenome/tests/main.nf.test.snap | 2 +- subworkflows/pasty/tests/main.nf.test.snap | 2 +- subworkflows/pbptyper/tests/main.nf.test.snap | 2 +- subworkflows/phispy/tests/main.nf.test.snap | 2 +- subworkflows/pirate/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../pneumocat/tests/main.nf.test.snap | 2 +- subworkflows/prokka/tests/main.nf.test.snap | 2 +- subworkflows/quast/tests/main.nf.test.snap | 2 +- subworkflows/rgi/tests/main.nf.test.snap | 2 +- subworkflows/roary/tests/main.nf.test.snap | 2 +- subworkflows/sccmec/tests/main.nf.test.snap | 2 +- subworkflows/scoary/tests/main.nf.test.snap | 2 +- subworkflows/scrubber/tests/main.nf.test.snap | 4 +- subworkflows/seqsero2/tests/main.nf.test.snap | 2 +- subworkflows/seroba/tests/main.nf.test.snap | 2 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- subworkflows/sistr/tests/main.nf.test.snap | 2 +- .../snippy/core/tests/main.nf.test.snap | 2 +- .../snippy/run/tests/main.nf.test.snap | 2 +- subworkflows/snpdists/tests/main.nf.test.snap | 2 +- subworkflows/spatyper/tests/main.nf.test.snap | 2 +- .../srahumanscrubber/tests/main.nf.test.snap | 2 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../staphopiasccmec/tests/main.nf.test.snap | 2 +- .../staphscan/tests/main.nf.test.snap | 2 +- .../stecfinder/tests/main.nf.test.snap | 2 +- subworkflows/stxtyper/tests/main.nf.test.snap | 2 +- subworkflows/sylph/tests/main.nf.test.snap | 2 +- subworkflows/tblastn/tests/main.nf.test.snap | 2 +- subworkflows/tblastx/tests/main.nf.test.snap | 2 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- subworkflows/teton/tests/main.nf.test.snap | 2 +- subworkflows/traitar/tests/main.nf.test | 16 +- subworkflows/traitar/tests/main.nf.test.snap | 13 +- tests/main.nf.test.snap | 1015 ++++++++++++++++- .../abricate/tests/main.nf.test.snap | 2 +- .../abritamr/tests/main.nf.test.snap | 2 +- .../agrvate/tests/main.nf.test.snap | 4 +- .../amrfinderplus/tests/main.nf.test.snap | 4 +- .../ariba/tests/main.nf.test.snap | 2 +- .../bakta/tests/main.nf.test.snap | 4 +- .../blastn/tests/main.nf.test.snap | 6 +- .../blastp/tests/main.nf.test.snap | 6 +- .../blastx/tests/main.nf.test.snap | 6 +- .../bracken/tests/main.nf.test.snap | 4 +- .../btyper3/tests/main.nf.test.snap | 2 +- .../busco/tests/main.nf.test.snap | 2 +- .../checkm/tests/main.nf.test.snap | 2 +- .../checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- .../ectyper/tests/main.nf.test.snap | 2 +- .../eggnog/tests/main.nf.test.snap | 2 +- .../emmtyper/tests/main.nf.test.snap | 4 +- .../fastani/tests/main.nf.test.snap | 6 +- .../gamma/tests/main.nf.test.snap | 2 +- .../genotyphi/tests/main.nf.test.snap | 2 +- .../gigatyper/tests/main.nf.test.snap | 2 +- .../gtdb/tests/main.nf.test.snap | 2 +- .../hicap/tests/main.nf.test.snap | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- .../ismapper/tests/main.nf.test.snap | 2 +- .../kleborate/tests/main.nf.test.snap | 2 +- .../kraken2/tests/main.nf.test.snap | 4 +- .../legsta/tests/main.nf.test.snap | 2 +- .../lissero/tests/main.nf.test.snap | 2 +- .../mashdist/tests/main.nf.test.snap | 2 +- .../mashtree/tests/main.nf.test.snap | 4 +- .../mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../merlin/tests/main.nf.test.snap | 4 +- .../midas/tests/main.nf.test.snap | 4 +- .../mlst/tests/main.nf.test.snap | 2 +- .../mobsuite/tests/main.nf.test.snap | 2 +- .../mykrobe/tests/main.nf.test.snap | 2 +- .../ngmaster/tests/main.nf.test.snap | 2 +- .../pangenome/tests/main.nf.test.snap | 12 +- .../pasty/tests/main.nf.test.snap | 2 +- .../pbptyper/tests/main.nf.test.snap | 2 +- .../phispy/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../pneumocat/tests/main.nf.test.snap | 2 +- .../prokka/tests/main.nf.test.snap | 2 +- .../quast/tests/main.nf.test.snap | 2 +- .../rgi/tests/main.nf.test.snap | 2 +- .../sccmec/tests/main.nf.test.snap | 4 +- .../scrubber/tests/main.nf.test.snap | 6 +- .../seqsero2/tests/main.nf.test.snap | 2 +- .../seroba/tests/main.nf.test.snap | 2 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- .../sistr/tests/main.nf.test.snap | 2 +- .../snippy/tests/main.nf.test.snap | 12 +- .../spatyper/tests/main.nf.test.snap | 4 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../staphscan/tests/main.nf.test.snap | 2 +- .../staphtyper/tests/main.nf.test.snap | 2 +- .../stecfinder/tests/main.nf.test.snap | 2 +- .../stxtyper/tests/main.nf.test.snap | 2 +- .../sylph/tests/main.nf.test.snap | 2 +- .../tblastn/tests/main.nf.test.snap | 4 +- .../tblastx/tests/main.nf.test.snap | 6 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- .../traitar/tests/main.nf.test.snap | 2 +- .../cleanyerreads/tests/main.nf.test.snap | 4 +- workflows/staphopia/tests/main.nf.test.snap | 2 +- workflows/teton/tests/main.nf.test.snap | 6 +- 254 files changed, 1415 insertions(+), 388 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f34de9fa..66927efb2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,16 +45,14 @@ sidebar_position: 5000 ### `Changed` - Updated bactopia-teton meta-package from 1.1.3 to 1.1.4 (includes deacon) +- Bumped required `bactopia-py` to `>=2.3.0` (conda `meta.yaml`) +- `bactopia gather` now downloads assemblies with `genome-dl` instead of `ncbi-genome-download` + - `--no_cache` is no longer available (`ncbi-genome-download` specific param) - `fastani`, `mashtree`, `pangenome` and `snippy` Bactopia Tools now download genomes with `genomedl` instead of `ncbigenomedownload` - `--kingdom` and `--keep_downloads` are no longer available to these tools - `--limit` now defaults to 100 for `--species` (previously unlimited) - - downloaded genomes are named by accession (`GCF_020736045.1`) rather than by NCBI's full - assembly filename (`GCF_020736045.1_ASM2073604v1_genomic`), which changes output paths and - tree/matrix labels - `snippy --accession` requires `--format genbank`, since Snippy needs an annotated reference -- `bactopia gather` now downloads assemblies with `genome-dl` instead of `ncbi-genome-download` - - `--no_cache` is no longer available (it only tuned `ncbi-genome-download`'s summary cache) - Deacon modules now use bactopia-teton container instead of standalone deacon container - Teton and scrubber workflows default to deacon instead of nohuman for host read removal - cleanyerreads workflow supports `--use_deacon` flag for host read removal diff --git a/catalog.json b/catalog.json index 5a5e8619d..adabeabed 100644 --- a/catalog.json +++ b/catalog.json @@ -1,8 +1,8 @@ { "version": "1.0", - "generated": "2026-07-28T22:44:08Z", + "generated": "2026-07-29T16:50:49Z", "bactopia_version": "4.1.0", - "bactopia_py_version": "2.2.0", + "bactopia_py_version": "2.3.0", "nf_bactopia_version": "2.1.6", "modules": { "abricate_run": { @@ -930,7 +930,8 @@ "r2", "se", "lr", - "scrub_report" + "scrub_report", + "json_summary" ], "emits_optional": [ "r1", diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 350d9944d..26cd3f4bf 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -17,7 +17,7 @@ requirements: - python >3.9,<3.14 - wget run: - - bactopia-py >=2.2.0 + - bactopia-py >=2.3.0 - conda >=25 - coreutils - mamba >=2 diff --git a/modules/abricate/run/tests/main.nf.test.snap b/modules/abricate/run/tests/main.nf.test.snap index 0150626c5..866d21abd 100644 --- a/modules/abricate/run/tests/main.nf.test.snap +++ b/modules/abricate/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,7baef5ee36e4b70a7227723d89bf97ea" ] ], - "timestamp": "2026-07-28T17:03:52.674364547", + "timestamp": "2026-07-29T01:28:24.214941395", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abricate/summary/tests/main.nf.test.snap b/modules/abricate/summary/tests/main.nf.test.snap index 0aca2db50..193599562 100644 --- a/modules/abricate/summary/tests/main.nf.test.snap +++ b/modules/abricate/summary/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,87422ca0c784de85ba93ac7352052d82" ] ], - "timestamp": "2026-07-28T17:03:57.316909203", + "timestamp": "2026-07-29T01:28:24.562552282", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abritamr/run/tests/main.nf.test.snap b/modules/abritamr/run/tests/main.nf.test.snap index 7dcc951fe..b2c0bf356 100644 --- a/modules/abritamr/run/tests/main.nf.test.snap +++ b/modules/abritamr/run/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-28T17:08:01.106751519", + "timestamp": "2026-07-29T01:32:45.809785745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-28T17:12:26.782352417", + "timestamp": "2026-07-29T01:37:03.995078677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/agrvate/tests/main.nf.test.snap b/modules/agrvate/tests/main.nf.test.snap index 3b477c2a5..8f434b286 100644 --- a/modules/agrvate/tests/main.nf.test.snap +++ b/modules/agrvate/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-28T17:04:04.297911813", + "timestamp": "2026-07-29T01:28:45.557959581", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-28T17:03:50.7369451", + "timestamp": "2026-07-29T01:28:29.676580462", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/amrfinderplus/run/tests/main.nf.test.snap b/modules/amrfinderplus/run/tests/main.nf.test.snap index 6acd0f633..962af0f7e 100644 --- a/modules/amrfinderplus/run/tests/main.nf.test.snap +++ b/modules/amrfinderplus/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-28T17:03:55.849652335", + "timestamp": "2026-07-29T01:28:44.847096965", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-28T17:04:18.867455838", + "timestamp": "2026-07-29T01:29:08.350914695", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ariba/run/tests/main.nf.test.snap b/modules/ariba/run/tests/main.nf.test.snap index 5d0e187bd..ab9fbd055 100644 --- a/modules/ariba/run/tests/main.nf.test.snap +++ b/modules/ariba/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2d20a87ab1578332cae79c947a52e8f8" ] ], - "timestamp": "2026-07-28T17:04:24.901542508", + "timestamp": "2026-07-29T01:28:59.378421092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/assembler/tests/main.nf.test.snap b/modules/bactopia/assembler/tests/main.nf.test.snap index 6036df2a9..61164b1ae 100644 --- a/modules/bactopia/assembler/tests/main.nf.test.snap +++ b/modules/bactopia/assembler/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:18:27.769304249", + "timestamp": "2026-07-29T01:43:03.413255267", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -41,7 +41,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:22:45.415299986", + "timestamp": "2026-07-29T01:47:26.293537587", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -65,7 +65,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:22:19.479954032", + "timestamp": "2026-07-29T01:46:59.67652929", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -89,7 +89,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:20:52.018603646", + "timestamp": "2026-07-29T01:45:27.327994741", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -113,7 +113,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:21:20.503729652", + "timestamp": "2026-07-29T01:45:57.813478176", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -137,7 +137,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:06:14.440697896", + "timestamp": "2026-07-29T01:30:53.217753604", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -161,7 +161,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:06:56.934841934", + "timestamp": "2026-07-29T01:31:33.844573405", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -185,7 +185,7 @@ "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" ] ], - "timestamp": "2026-07-28T17:11:00.59649405", + "timestamp": "2026-07-29T01:35:24.570380526", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/gather/tests/main.nf.test.snap b/modules/bactopia/gather/tests/main.nf.test.snap index 83c91d7e9..f9bb23c5d 100644 --- a/modules/bactopia/gather/tests/main.nf.test.snap +++ b/modules/bactopia/gather/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:04:53.278324761", + "timestamp": "2026-07-29T01:29:33.799764907", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:05:18.23295091", + "timestamp": "2026-07-29T01:29:57.878211735", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -70,7 +70,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:07:02.236536952", + "timestamp": "2026-07-29T01:31:40.907151631", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:06:40.90510727", + "timestamp": "2026-07-29T01:31:19.73009397", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -121,7 +121,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:05:54.566859301", + "timestamp": "2026-07-29T01:30:34.967253801", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:06:16.525974229", + "timestamp": "2026-07-29T01:30:56.298486348", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -173,7 +173,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:04:06.350260305", + "timestamp": "2026-07-29T01:28:47.975892113", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -199,7 +199,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-28T17:04:29.711658336", + "timestamp": "2026-07-29T01:29:11.193972235", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/qc/tests/main.nf.test.snap b/modules/bactopia/qc/tests/main.nf.test.snap index 6134b07e1..bbd592de9 100644 --- a/modules/bactopia/qc/tests/main.nf.test.snap +++ b/modules/bactopia/qc/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-07-28T17:05:14.605830198", + "timestamp": "2026-07-29T01:29:53.240079953", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -41,7 +41,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-07-28T17:06:17.640161203", + "timestamp": "2026-07-29T01:30:53.187400287", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -65,7 +65,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-07-28T17:08:57.462133171", + "timestamp": "2026-07-29T01:33:36.18953171", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -89,7 +89,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-07-28T17:07:08.017750891", + "timestamp": "2026-07-29T01:31:45.972044885", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -113,7 +113,7 @@ "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" ] ], - "timestamp": "2026-07-28T17:09:37.663643786", + "timestamp": "2026-07-29T01:34:13.427660919", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/sketcher/tests/main.nf.test.snap b/modules/bactopia/sketcher/tests/main.nf.test.snap index 1c48bb473..19caaf410 100644 --- a/modules/bactopia/sketcher/tests/main.nf.test.snap +++ b/modules/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,559fcd38f7410952b8da3f25f165d6fd" ] ], - "timestamp": "2026-07-28T17:06:23.390221639", + "timestamp": "2026-07-29T01:31:45.215794434", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/teton/tests/main.nf.test.snap b/modules/bactopia/teton/tests/main.nf.test.snap index 2d0808857..b33c23d3b 100644 --- a/modules/bactopia/teton/tests/main.nf.test.snap +++ b/modules/bactopia/teton/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-28T17:03:50.235609268", + "timestamp": "2026-07-29T01:28:35.254165018", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-28T17:04:03.989943423", + "timestamp": "2026-07-29T01:28:51.543511604", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bakta/run/tests/main.nf.test.snap b/modules/bakta/run/tests/main.nf.test.snap index 7b9f85653..1b2575d9a 100644 --- a/modules/bakta/run/tests/main.nf.test.snap +++ b/modules/bakta/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-28T17:08:03.063640921", + "timestamp": "2026-07-29T01:32:31.402053192", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-28T17:11:00.780109231", + "timestamp": "2026-07-29T01:35:20.61960942", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastn/tests/main.nf.test.snap b/modules/blast/blastn/tests/main.nf.test.snap index 67cb717f4..34cd85883 100644 --- a/modules/blast/blastn/tests/main.nf.test.snap +++ b/modules/blast/blastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,45d0dac48620078713131f03b02bd14a" ] ], - "timestamp": "2026-07-28T17:03:46.984825239", + "timestamp": "2026-07-29T01:28:25.15166746", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastp/tests/main.nf.test.snap b/modules/blast/blastp/tests/main.nf.test.snap index 36f0e78a9..ce7546b71 100644 --- a/modules/blast/blastp/tests/main.nf.test.snap +++ b/modules/blast/blastp/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,617451a4191edeef7d2c7fb101c1ac14" ] ], - "timestamp": "2026-07-28T17:03:47.934334506", + "timestamp": "2026-07-29T01:28:25.530081089", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastx/tests/main.nf.test.snap b/modules/blast/blastx/tests/main.nf.test.snap index 93d635b4b..3c7796fcd 100644 --- a/modules/blast/blastx/tests/main.nf.test.snap +++ b/modules/blast/blastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6a3a4c2a4204ac747af921720f265d86" ] ], - "timestamp": "2026-07-28T17:03:53.49461217", + "timestamp": "2026-07-29T01:28:29.086481152", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastn/tests/main.nf.test.snap b/modules/blast/tblastn/tests/main.nf.test.snap index 54132b077..d96fa311a 100644 --- a/modules/blast/tblastn/tests/main.nf.test.snap +++ b/modules/blast/tblastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,24c7db9cd7b317dcf8ad2057a04b2860" ] ], - "timestamp": "2026-07-28T17:03:56.595666724", + "timestamp": "2026-07-29T01:28:28.223585438", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastx/tests/main.nf.test.snap b/modules/blast/tblastx/tests/main.nf.test.snap index d83923efb..135ece600 100644 --- a/modules/blast/tblastx/tests/main.nf.test.snap +++ b/modules/blast/tblastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2d402efb20baa10e7b3af88ef3f2312d" ] ], - "timestamp": "2026-07-28T17:03:48.342241056", + "timestamp": "2026-07-29T01:28:23.804195768", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bracken/tests/main.nf.test.snap b/modules/bracken/tests/main.nf.test.snap index db75e2f15..05f202cb3 100644 --- a/modules/bracken/tests/main.nf.test.snap +++ b/modules/bracken/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" ] ], - "timestamp": "2026-07-28T17:04:36.177909247", + "timestamp": "2026-07-29T01:29:08.625794562", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" ] ], - "timestamp": "2026-07-28T17:10:34.742056394", + "timestamp": "2026-07-29T01:32:44.608829119", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/btyper3/tests/main.nf.test.snap b/modules/btyper3/tests/main.nf.test.snap index 4a8f328dd..17620e7da 100644 --- a/modules/btyper3/tests/main.nf.test.snap +++ b/modules/btyper3/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-28T17:07:30.205684975", + "timestamp": "2026-07-29T01:32:06.398267795", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-28T17:05:35.854705389", + "timestamp": "2026-07-29T01:30:08.996194966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/busco/tests/main.nf.test.snap b/modules/busco/tests/main.nf.test.snap index a3552790c..ea4401a8f 100644 --- a/modules/busco/tests/main.nf.test.snap +++ b/modules/busco/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-28T19:41:02.471307985", + "timestamp": "2026-07-29T01:29:39.626561878", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-28T19:40:46.603081275", + "timestamp": "2026-07-29T01:29:00.704051991", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm/lineagewf/tests/main.nf.test.snap b/modules/checkm/lineagewf/tests/main.nf.test.snap index 3f1a7e305..5cd23ea4d 100644 --- a/modules/checkm/lineagewf/tests/main.nf.test.snap +++ b/modules/checkm/lineagewf/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-28T17:12:42.455049596", + "timestamp": "2026-07-29T01:37:46.356450791", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-28T17:14:43.147805748", + "timestamp": "2026-07-29T01:39:46.180001117", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm2/predict/tests/main.nf.test.snap b/modules/checkm2/predict/tests/main.nf.test.snap index d9f568359..e4317f3f3 100644 --- a/modules/checkm2/predict/tests/main.nf.test.snap +++ b/modules/checkm2/predict/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-28T17:13:56.807206506", + "timestamp": "2026-07-29T01:38:34.282334837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-28T17:08:57.106485631", + "timestamp": "2026-07-29T01:33:33.954236979", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clermontyping/tests/main.nf.test.snap b/modules/clermontyping/tests/main.nf.test.snap index b4dfde6f9..138cf4bf0 100644 --- a/modules/clermontyping/tests/main.nf.test.snap +++ b/modules/clermontyping/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-28T17:04:48.741988928", + "timestamp": "2026-07-29T01:29:31.436003132", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-28T17:04:11.749476", + "timestamp": "2026-07-29T01:28:50.957786328", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clonalframeml/tests/main.nf.test.snap b/modules/clonalframeml/tests/main.nf.test.snap index 735271317..7ac3faa34 100644 --- a/modules/clonalframeml/tests/main.nf.test.snap +++ b/modules/clonalframeml/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-28T17:05:01.420153092", + "timestamp": "2026-07-29T01:29:41.445652493", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-28T17:06:21.64403345", + "timestamp": "2026-07-29T01:31:00.864624347", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/concat/tests/main.nf.test.snap b/modules/csvtk/concat/tests/main.nf.test.snap index 19d6d1d70..d22f6ebd3 100644 --- a/modules/csvtk/concat/tests/main.nf.test.snap +++ b/modules/csvtk/concat/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-28T17:03:53.009649866", + "timestamp": "2026-07-29T01:28:25.734452779", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-28T17:04:06.155187775", + "timestamp": "2026-07-29T01:28:38.021624805", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/join/tests/main.nf.test.snap b/modules/csvtk/join/tests/main.nf.test.snap index 389b58c4e..d82bafa94 100644 --- a/modules/csvtk/join/tests/main.nf.test.snap +++ b/modules/csvtk/join/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-28T17:03:47.830304788", + "timestamp": "2026-07-29T01:28:28.735880068", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-28T17:04:02.012883981", + "timestamp": "2026-07-29T01:28:44.215441107", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/deacon/filter/tests/main.nf.test.snap b/modules/deacon/filter/tests/main.nf.test.snap index 419b5fbba..fc237985d 100644 --- a/modules/deacon/filter/tests/main.nf.test.snap +++ b/modules/deacon/filter/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-28T17:05:10.605107483", + "timestamp": "2026-07-29T01:29:57.869746208", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-28T17:04:35.120671774", + "timestamp": "2026-07-29T01:29:23.017586857", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-28T17:04:02.976247105", + "timestamp": "2026-07-29T01:28:49.029308216", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/defensefinder/run/tests/main.nf.test.snap b/modules/defensefinder/run/tests/main.nf.test.snap index 15b335f5a..8d6bfa001 100644 --- a/modules/defensefinder/run/tests/main.nf.test.snap +++ b/modules/defensefinder/run/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,96378138554cc40b07841aed5efb3e7d" ] ], - "timestamp": "2026-07-28T17:04:31.48211912", + "timestamp": "2026-07-29T01:29:02.802693936", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ectyper/tests/main.nf.test.snap b/modules/ectyper/tests/main.nf.test.snap index 5ee290000..01e3fa44d 100644 --- a/modules/ectyper/tests/main.nf.test.snap +++ b/modules/ectyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-28T17:05:03.748844858", + "timestamp": "2026-07-29T01:29:25.338543091", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-28T17:04:23.970768955", + "timestamp": "2026-07-29T01:28:46.893787037", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/eggnog/mapper/tests/main.nf.test.snap b/modules/eggnog/mapper/tests/main.nf.test.snap index 6c9bce1ec..2bab455ad 100644 --- a/modules/eggnog/mapper/tests/main.nf.test.snap +++ b/modules/eggnog/mapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,591b018c5d70f26267582a8932b0271d" ] ], - "timestamp": "2026-07-28T17:17:26.374518532", + "timestamp": "2026-07-29T01:42:09.932051896", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,591b018c5d70f26267582a8932b0271d" ] ], - "timestamp": "2026-07-28T17:21:41.280155523", + "timestamp": "2026-07-29T01:46:27.638181705", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/emmtyper/tests/main.nf.test.snap b/modules/emmtyper/tests/main.nf.test.snap index 60bfa469f..1e31324a7 100644 --- a/modules/emmtyper/tests/main.nf.test.snap +++ b/modules/emmtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-28T17:04:16.232229719", + "timestamp": "2026-07-29T01:28:53.180287944", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-28T17:04:33.141894812", + "timestamp": "2026-07-29T01:29:08.83918294", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-28T17:03:59.67691452", + "timestamp": "2026-07-29T01:28:37.398509688", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/fastani/tests/main.nf.test.snap b/modules/fastani/tests/main.nf.test.snap index 9bf90a5ab..37a726807 100644 --- a/modules/fastani/tests/main.nf.test.snap +++ b/modules/fastani/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-28T17:03:48.547821427", + "timestamp": "2026-07-29T01:28:29.889659595", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-28T17:04:03.686628869", + "timestamp": "2026-07-29T01:28:45.072480668", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gamma/tests/main.nf.test.snap b/modules/gamma/tests/main.nf.test.snap index 20750d6d1..a72085baf 100644 --- a/modules/gamma/tests/main.nf.test.snap +++ b/modules/gamma/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-28T17:03:51.924823231", + "timestamp": "2026-07-29T01:28:37.396500578", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-28T17:04:05.726715129", + "timestamp": "2026-07-29T01:28:53.37689059", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genomedl/tests/main.nf.test.snap b/modules/genomedl/tests/main.nf.test.snap index 874a2d322..eee2ed32e 100644 --- a/modules/genomedl/tests/main.nf.test.snap +++ b/modules/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-28T17:04:12.889654592", + "timestamp": "2026-07-29T01:28:56.180701277", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-28T17:03:54.906366097", + "timestamp": "2026-07-29T01:28:37.710267022", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-28T17:04:29.596345709", + "timestamp": "2026-07-29T01:29:16.386057829", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genotyphi/parse/tests/main.nf.test.snap b/modules/genotyphi/parse/tests/main.nf.test.snap index 59995b02c..a0507db27 100644 --- a/modules/genotyphi/parse/tests/main.nf.test.snap +++ b/modules/genotyphi/parse/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,359680888d6e4e84784879e6e92c3439" ] ], - "timestamp": "2026-07-28T17:03:53.300346668", + "timestamp": "2026-07-29T01:28:26.188471089", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gigatyper/tests/main.nf.test.snap b/modules/gigatyper/tests/main.nf.test.snap index bd55af5dc..37b9ddbe4 100644 --- a/modules/gigatyper/tests/main.nf.test.snap +++ b/modules/gigatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ae98787b0c6ddf8f10515b895570a41a" ] ], - "timestamp": "2026-07-28T17:04:03.754486026", + "timestamp": "2026-07-29T01:28:37.418545613", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/gtdbtk/classifywf/tests/main.nf.test.snap index 7c62a9468..f4b1ac14f 100644 --- a/modules/gtdbtk/classifywf/tests/main.nf.test.snap +++ b/modules/gtdbtk/classifywf/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,7cb27f0b82d34e40565279ff91f60fda" ] ], - "timestamp": "2026-07-28T17:08:44.100864413", + "timestamp": "2026-07-29T01:33:27.092172684", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gubbins/tests/main.nf.test.snap b/modules/gubbins/tests/main.nf.test.snap index c13623d80..dfc575fa0 100644 --- a/modules/gubbins/tests/main.nf.test.snap +++ b/modules/gubbins/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-07-28T17:04:08.285562828", + "timestamp": "2026-07-29T01:28:44.679935189", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-07-28T17:04:45.743885757", + "timestamp": "2026-07-29T01:29:19.396599431", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hicap/tests/main.nf.test.snap b/modules/hicap/tests/main.nf.test.snap index f76edd6bd..964a09e54 100644 --- a/modules/hicap/tests/main.nf.test.snap +++ b/modules/hicap/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-28T17:05:05.438707309", + "timestamp": "2026-07-29T01:29:41.345999565", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-28T17:04:23.651765181", + "timestamp": "2026-07-29T01:28:59.426370845", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-28T17:06:19.426592773", + "timestamp": "2026-07-29T01:30:55.41454133", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-28T17:05:43.02612693", + "timestamp": "2026-07-29T01:30:19.146421722", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hpsuissero/tests/main.nf.test.snap b/modules/hpsuissero/tests/main.nf.test.snap index 85ae7eecd..9c7cc698d 100644 --- a/modules/hpsuissero/tests/main.nf.test.snap +++ b/modules/hpsuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-28T17:04:15.224903196", + "timestamp": "2026-07-29T01:28:44.901139419", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-28T17:03:59.195283123", + "timestamp": "2026-07-29T01:28:28.575819213", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/iqtree/tests/main.nf.test.snap b/modules/iqtree/tests/main.nf.test.snap index ee623057c..2f99cee2c 100644 --- a/modules/iqtree/tests/main.nf.test.snap +++ b/modules/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-28T17:04:22.270835292", + "timestamp": "2026-07-29T01:28:53.673412493", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-28T17:04:06.216512741", + "timestamp": "2026-07-29T01:28:37.947807747", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ismapper/tests/main.nf.test.snap b/modules/ismapper/tests/main.nf.test.snap index c22cfca05..577203826 100644 --- a/modules/ismapper/tests/main.nf.test.snap +++ b/modules/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,bbe2280116459026bfc2304b2b6c0f5f" ] ], - "timestamp": "2026-07-28T17:04:48.918091806", + "timestamp": "2026-07-29T01:29:29.79232796", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kleborate/tests/main.nf.test.snap b/modules/kleborate/tests/main.nf.test.snap index 997a491b0..063f7bfa3 100644 --- a/modules/kleborate/tests/main.nf.test.snap +++ b/modules/kleborate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9511fd36659702fc20722109151dca4b" ] ], - "timestamp": "2026-07-28T17:04:28.2033193", + "timestamp": "2026-07-29T01:29:08.674898666", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kraken2/tests/main.nf.test.snap b/modules/kraken2/tests/main.nf.test.snap index 565b8164f..c2a6f0073 100644 --- a/modules/kraken2/tests/main.nf.test.snap +++ b/modules/kraken2/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-28T17:10:02.058157343", + "timestamp": "2026-07-29T01:32:39.700156655", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-28T17:04:05.745055868", + "timestamp": "2026-07-29T01:29:02.901636556", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/legsta/tests/main.nf.test.snap b/modules/legsta/tests/main.nf.test.snap index 25421029e..0d4a4d07f 100644 --- a/modules/legsta/tests/main.nf.test.snap +++ b/modules/legsta/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1ea80a08aa0a9efc6d82ffa9e668ad6d" ] ], - "timestamp": "2026-07-28T17:03:49.761469566", + "timestamp": "2026-07-29T01:28:26.639588521", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/lissero/tests/main.nf.test.snap b/modules/lissero/tests/main.nf.test.snap index 706772e8b..10925ff96 100644 --- a/modules/lissero/tests/main.nf.test.snap +++ b/modules/lissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-28T17:04:19.361243979", + "timestamp": "2026-07-29T01:28:49.53199812", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-28T17:04:02.075983877", + "timestamp": "2026-07-29T01:28:31.309469065", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mash/dist/tests/main.nf.test.snap b/modules/mash/dist/tests/main.nf.test.snap index b2b1dd1d5..26a22a31d 100644 --- a/modules/mash/dist/tests/main.nf.test.snap +++ b/modules/mash/dist/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-28T17:04:09.318813499", + "timestamp": "2026-07-29T01:28:42.959541898", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-28T17:03:54.746407145", + "timestamp": "2026-07-29T01:28:27.866033658", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mashtree/tests/main.nf.test.snap b/modules/mashtree/tests/main.nf.test.snap index 1fdd9afcb..f828342ba 100644 --- a/modules/mashtree/tests/main.nf.test.snap +++ b/modules/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,6d51bcb025e39e73864f2236b1ce99e9" ] ], - "timestamp": "2026-07-28T17:03:51.860130438", + "timestamp": "2026-07-29T01:28:33.892279973", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mcroni/tests/main.nf.test.snap b/modules/mcroni/tests/main.nf.test.snap index 856b55cea..146153a4d 100644 --- a/modules/mcroni/tests/main.nf.test.snap +++ b/modules/mcroni/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-28T17:04:12.006871014", + "timestamp": "2026-07-29T01:28:52.637121097", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-28T17:03:55.324984592", + "timestamp": "2026-07-29T01:28:35.605702524", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/meningotype/tests/main.nf.test.snap b/modules/meningotype/tests/main.nf.test.snap index a3942cde4..3a595a1d8 100644 --- a/modules/meningotype/tests/main.nf.test.snap +++ b/modules/meningotype/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-28T17:04:10.175706031", + "timestamp": "2026-07-29T01:28:41.488960841", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-28T17:03:53.421375832", + "timestamp": "2026-07-29T01:28:26.183236981", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/merlin/dist/tests/main.nf.test.snap b/modules/merlin/dist/tests/main.nf.test.snap index b6ec83a0b..0e7acddf6 100644 --- a/modules/merlin/dist/tests/main.nf.test.snap +++ b/modules/merlin/dist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-28T17:05:05.379345937", + "timestamp": "2026-07-29T01:29:36.578914755", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-28T17:06:25.456477033", + "timestamp": "2026-07-29T01:30:57.258068201", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/midas/species/tests/main.nf.test.snap b/modules/midas/species/tests/main.nf.test.snap index d6b2485ec..799a33167 100644 --- a/modules/midas/species/tests/main.nf.test.snap +++ b/modules/midas/species/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-28T17:10:58.232093107", + "timestamp": "2026-07-29T01:35:16.988424548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-28T17:11:55.860507334", + "timestamp": "2026-07-29T01:36:15.146887371", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mlst/tests/main.nf.test.snap b/modules/mlst/tests/main.nf.test.snap index 977b49d95..bddff9fa9 100644 --- a/modules/mlst/tests/main.nf.test.snap +++ b/modules/mlst/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6515f9242cdb83b9c720f39ce67a528f" ] ], - "timestamp": "2026-07-28T17:03:51.417063793", + "timestamp": "2026-07-29T01:28:30.214334872", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mobsuite/recon/tests/main.nf.test.snap b/modules/mobsuite/recon/tests/main.nf.test.snap index 4dbbdfd2b..526fc5ffa 100644 --- a/modules/mobsuite/recon/tests/main.nf.test.snap +++ b/modules/mobsuite/recon/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-28T17:07:55.232262612", + "timestamp": "2026-07-29T01:32:39.788411473", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -40,7 +40,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-28T17:06:46.930322714", + "timestamp": "2026-07-29T01:31:32.174679544", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-28T17:05:12.990479906", + "timestamp": "2026-07-29T01:29:56.247980884", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mykrobe/predict/tests/main.nf.test.snap b/modules/mykrobe/predict/tests/main.nf.test.snap index e1b4fc2e7..981a3a4c8 100644 --- a/modules/mykrobe/predict/tests/main.nf.test.snap +++ b/modules/mykrobe/predict/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,3756fdfbed62cef8782098468ef3da9d" ] ], - "timestamp": "2026-07-28T17:03:59.629821371", + "timestamp": "2026-07-29T01:28:37.396382827", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ngmaster/tests/main.nf.test.snap b/modules/ngmaster/tests/main.nf.test.snap index bbeeb6cf3..70486d37b 100644 --- a/modules/ngmaster/tests/main.nf.test.snap +++ b/modules/ngmaster/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-28T17:03:53.644612074", + "timestamp": "2026-07-29T01:28:32.227397767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-28T17:04:15.788207516", + "timestamp": "2026-07-29T01:28:55.706135945", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/nohuman/run/tests/main.nf.test.snap b/modules/nohuman/run/tests/main.nf.test.snap index 74637d4f0..3d4bede4c 100644 --- a/modules/nohuman/run/tests/main.nf.test.snap +++ b/modules/nohuman/run/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-28T17:15:29.132571832", + "timestamp": "2026-07-29T01:40:15.078503284", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-28T17:19:06.11822473", + "timestamp": "2026-07-29T01:43:54.729970861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-28T17:10:47.757626415", + "timestamp": "2026-07-29T01:35:29.001683385", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/panaroo/run/tests/main.nf.test.snap b/modules/panaroo/run/tests/main.nf.test.snap index f10e6e127..1ccd7bcce 100644 --- a/modules/panaroo/run/tests/main.nf.test.snap +++ b/modules/panaroo/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e6a0f1e191dcfb92fab2a7d68063c31d" ] ], - "timestamp": "2026-07-28T19:41:35.651447042", + "timestamp": "2026-07-29T01:30:14.863586619", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pasty/tests/main.nf.test.snap b/modules/pasty/tests/main.nf.test.snap index b7d6eb68b..3cdce4b7c 100644 --- a/modules/pasty/tests/main.nf.test.snap +++ b/modules/pasty/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,275841ecfb594907dd941a31a5e5f171" ] ], - "timestamp": "2026-07-28T17:04:01.864693232", + "timestamp": "2026-07-29T01:28:30.918704318", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pbptyper/tests/main.nf.test.snap b/modules/pbptyper/tests/main.nf.test.snap index b15a9bac3..658bb3bb8 100644 --- a/modules/pbptyper/tests/main.nf.test.snap +++ b/modules/pbptyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,be74af83bdcf74f71056df98990fdeda" ] ], - "timestamp": "2026-07-28T17:04:40.027774057", + "timestamp": "2026-07-29T01:29:10.577383619", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/phispy/tests/main.nf.test.snap b/modules/phispy/tests/main.nf.test.snap index b5a1c54b8..55da66ef7 100644 --- a/modules/phispy/tests/main.nf.test.snap +++ b/modules/phispy/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,97542c4eb1d90b2b0a0375c916b75dc5" ] ], - "timestamp": "2026-07-28T17:06:15.020944732", + "timestamp": "2026-07-29T01:30:56.561524725", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pirate/tests/main.nf.test.snap b/modules/pirate/tests/main.nf.test.snap index 03b5e4f78..a58376b56 100644 --- a/modules/pirate/tests/main.nf.test.snap +++ b/modules/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,ce4d40e2b87e2e5cac6e755fcb0c023b" ] ], - "timestamp": "2026-07-28T17:07:05.838150755", + "timestamp": "2026-07-29T01:31:40.088702729", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/plasmidfinder/tests/main.nf.test.snap b/modules/plasmidfinder/tests/main.nf.test.snap index 6cf93371a..45c44dfbf 100644 --- a/modules/plasmidfinder/tests/main.nf.test.snap +++ b/modules/plasmidfinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-28T17:04:09.34637667", + "timestamp": "2026-07-29T01:29:01.42436456", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-28T17:04:31.879284068", + "timestamp": "2026-07-29T01:29:25.033686013", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pneumocat/tests/main.nf.test.snap b/modules/pneumocat/tests/main.nf.test.snap index 7c2aa5ba9..123ebd711 100644 --- a/modules/pneumocat/tests/main.nf.test.snap +++ b/modules/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf" ] ], - "timestamp": "2026-07-28T17:04:10.996091644", + "timestamp": "2026-07-29T01:29:13.655966628", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/prokka/tests/main.nf.test.snap b/modules/prokka/tests/main.nf.test.snap index 4d069c974..4f8cf62be 100644 --- a/modules/prokka/tests/main.nf.test.snap +++ b/modules/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-28T17:05:06.405344361", + "timestamp": "2026-07-29T01:29:47.874375257", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-28T17:05:40.570755671", + "timestamp": "2026-07-29T01:30:20.662561693", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-28T17:06:26.671459009", + "timestamp": "2026-07-29T01:31:09.500747676", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/quast/tests/main.nf.test.snap b/modules/quast/tests/main.nf.test.snap index 317c69148..c8d7e24fd 100644 --- a/modules/quast/tests/main.nf.test.snap +++ b/modules/quast/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-07-28T17:05:23.753301259", + "timestamp": "2026-07-29T01:30:02.385132653", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-07-28T17:05:01.575708819", + "timestamp": "2026-07-29T01:29:39.532960005", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" ] ], - "timestamp": "2026-07-28T17:04:36.267729238", + "timestamp": "2026-07-29T01:29:14.30005886", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/heatmap/tests/main.nf.test.snap b/modules/rgi/heatmap/tests/main.nf.test.snap index f401efa7f..617be3ff3 100644 --- a/modules/rgi/heatmap/tests/main.nf.test.snap +++ b/modules/rgi/heatmap/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,85fd687a901fef3c05e188fe49391c68" ] ], - "timestamp": "2026-07-28T17:04:40.292532375", + "timestamp": "2026-07-29T01:29:19.004197858", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/main/module.config b/modules/rgi/main/module.config index 554d70add..e622fd5a0 100644 --- a/modules/rgi/main/module.config +++ b/modules/rgi/main/module.config @@ -3,9 +3,9 @@ params { rgi_category = "" rgi_cluster = "" rgi_display = "plain" - rgi_include_nudge = false rgi_frequency = false rgi_include_loose = false + rgi_include_nudge = false rgi_use_diamond = false } diff --git a/modules/rgi/main/tests/main.nf.test.snap b/modules/rgi/main/tests/main.nf.test.snap index 5e4c9819a..81262c018 100644 --- a/modules/rgi/main/tests/main.nf.test.snap +++ b/modules/rgi/main/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-28T18:26:02.309171001", + "timestamp": "2026-07-29T01:30:14.523232332", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-28T18:27:17.03098611", + "timestamp": "2026-07-29T01:32:51.787211419", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-28T18:26:38.946091259", + "timestamp": "2026-07-29T01:31:32.600476615", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/roary/tests/main.nf.test.snap b/modules/roary/tests/main.nf.test.snap index 37718da98..1c1045866 100644 --- a/modules/roary/tests/main.nf.test.snap +++ b/modules/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,80c99c1b38b33ebcb7925eabba7ca2eb" ] ], - "timestamp": "2026-07-28T17:06:06.835395759", + "timestamp": "2026-07-29T01:30:43.478592884", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sccmec/tests/main.nf.test.snap b/modules/sccmec/tests/main.nf.test.snap index 939020664..4695bc6e6 100644 --- a/modules/sccmec/tests/main.nf.test.snap +++ b/modules/sccmec/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" ] ], - "timestamp": "2026-07-28T17:04:42.233854202", + "timestamp": "2026-07-29T01:29:16.80545439", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" ] ], - "timestamp": "2026-07-28T17:05:02.684305186", + "timestamp": "2026-07-29T01:29:37.633384608", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/scoary/tests/main.nf.test.snap b/modules/scoary/tests/main.nf.test.snap index 2a4340347..058f73ae1 100644 --- a/modules/scoary/tests/main.nf.test.snap +++ b/modules/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,f8f8a2300f84de4e8184c9dd33579ccd" ] ], - "timestamp": "2026-07-28T17:04:39.878685538", + "timestamp": "2026-07-29T01:29:13.87691542", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seqsero2/tests/main.nf.test.snap b/modules/seqsero2/tests/main.nf.test.snap index 951b747c7..88ae69e4a 100644 --- a/modules/seqsero2/tests/main.nf.test.snap +++ b/modules/seqsero2/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-28T17:04:56.44659963", + "timestamp": "2026-07-29T01:29:32.01873251", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-28T17:04:40.02602688", + "timestamp": "2026-07-29T01:29:15.566965302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seroba/run/tests/main.nf.test.snap b/modules/seroba/run/tests/main.nf.test.snap index 958e3ad60..d4cc4bf6a 100644 --- a/modules/seroba/run/tests/main.nf.test.snap +++ b/modules/seroba/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,e485bb335ccae3f5e5f24f35690633d3" ] ], - "timestamp": "2026-07-28T17:05:10.585666494", + "timestamp": "2026-07-29T01:29:52.632361366", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigapass/tests/main.nf.test.snap b/modules/shigapass/tests/main.nf.test.snap index 62010e8e9..2b9d684e7 100644 --- a/modules/shigapass/tests/main.nf.test.snap +++ b/modules/shigapass/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-28T17:04:53.170596966", + "timestamp": "2026-07-29T01:29:34.756318038", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-28T17:05:20.818727304", + "timestamp": "2026-07-29T01:30:00.877488575", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigatyper/tests/main.nf.test.snap b/modules/shigatyper/tests/main.nf.test.snap index 093064a7b..69a3f10ae 100644 --- a/modules/shigatyper/tests/main.nf.test.snap +++ b/modules/shigatyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,5546505c7719718340a0cd98ece587d8" ] ], - "timestamp": "2026-07-28T17:04:47.911451164", + "timestamp": "2026-07-29T01:29:27.06297208", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigeifinder/tests/main.nf.test.snap b/modules/shigeifinder/tests/main.nf.test.snap index 06b0e55de..e2207d673 100644 --- a/modules/shigeifinder/tests/main.nf.test.snap +++ b/modules/shigeifinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-28T17:04:57.786169176", + "timestamp": "2026-07-29T01:29:40.833944402", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-28T17:04:42.412647302", + "timestamp": "2026-07-29T01:29:25.24104086", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sistr/tests/main.nf.test.snap b/modules/sistr/tests/main.nf.test.snap index 1aecda476..0ca559fb6 100644 --- a/modules/sistr/tests/main.nf.test.snap +++ b/modules/sistr/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-28T17:05:16.274198697", + "timestamp": "2026-07-29T01:30:01.819167841", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-28T17:05:59.227307511", + "timestamp": "2026-07-29T01:30:43.557274508", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/core/tests/main.nf.test.snap b/modules/snippy/core/tests/main.nf.test.snap index d20b48d20..2650ad6cc 100644 --- a/modules/snippy/core/tests/main.nf.test.snap +++ b/modules/snippy/core/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,af05caa4daa181fbe9d7bf82d3383d93" ] ], - "timestamp": "2026-07-28T17:04:53.721386457", + "timestamp": "2026-07-29T01:29:37.074346963", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/run/tests/main.nf.test.snap b/modules/snippy/run/tests/main.nf.test.snap index b47d6a618..ab632c1a6 100644 --- a/modules/snippy/run/tests/main.nf.test.snap +++ b/modules/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-28T17:06:03.703638294", + "timestamp": "2026-07-29T01:30:41.279350699", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-28T17:05:24.72141497", + "timestamp": "2026-07-29T01:30:02.591273048", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snpdists/tests/main.nf.test.snap b/modules/snpdists/tests/main.nf.test.snap index 8603b959c..6040dcff2 100644 --- a/modules/snpdists/tests/main.nf.test.snap +++ b/modules/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,944b6ecf9bf11c38b608ae08b36d5e2d" ] ], - "timestamp": "2026-07-28T17:04:56.460770293", + "timestamp": "2026-07-29T01:29:38.075792054", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/spatyper/tests/main.nf.test.snap b/modules/spatyper/tests/main.nf.test.snap index 4f5cc54be..5718e7f24 100644 --- a/modules/spatyper/tests/main.nf.test.snap +++ b/modules/spatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-28T17:05:27.906825448", + "timestamp": "2026-07-29T01:30:05.767014154", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-28T17:05:07.974904548", + "timestamp": "2026-07-29T01:29:45.843982744", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap index 441fbcf6c..94a5bf1fb 100644 --- a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap +++ b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-28T17:07:04.704034393", + "timestamp": "2026-07-29T01:31:42.097451028", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-28T17:06:15.637730118", + "timestamp": "2026-07-29T01:30:53.448245388", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ssuissero/tests/main.nf.test.snap b/modules/ssuissero/tests/main.nf.test.snap index 3f6a5a4b9..2d24a5872 100644 --- a/modules/ssuissero/tests/main.nf.test.snap +++ b/modules/ssuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-28T17:05:03.055657376", + "timestamp": "2026-07-29T01:29:42.832734695", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-28T17:05:16.698142582", + "timestamp": "2026-07-29T01:29:56.850525477", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphopiasccmec/tests/main.nf.test.snap b/modules/staphopiasccmec/tests/main.nf.test.snap index 5b73071c8..62782f018 100644 --- a/modules/staphopiasccmec/tests/main.nf.test.snap +++ b/modules/staphopiasccmec/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-28T17:05:04.955792698", + "timestamp": "2026-07-29T01:29:44.925199169", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-28T17:05:18.97449695", + "timestamp": "2026-07-29T01:29:59.641091224", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphscan/tests/main.nf.test.snap b/modules/staphscan/tests/main.nf.test.snap index cd8c4b23b..038f09cca 100644 --- a/modules/staphscan/tests/main.nf.test.snap +++ b/modules/staphscan/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,251f3e6b35be5f660d5fc8bc8456bde6" ] ], - "timestamp": "2026-07-28T17:05:19.361127758", + "timestamp": "2026-07-29T01:30:00.265720929", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stecfinder/tests/main.nf.test.snap b/modules/stecfinder/tests/main.nf.test.snap index da2337601..56c4318d3 100644 --- a/modules/stecfinder/tests/main.nf.test.snap +++ b/modules/stecfinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-28T17:05:37.98973119", + "timestamp": "2026-07-29T01:30:20.622055724", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-28T17:05:22.061014948", + "timestamp": "2026-07-29T01:30:05.008808748", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-28T17:05:06.285732415", + "timestamp": "2026-07-29T01:29:50.297484471", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stxtyper/tests/main.nf.test.snap b/modules/stxtyper/tests/main.nf.test.snap index 4083d438f..33726ead9 100644 --- a/modules/stxtyper/tests/main.nf.test.snap +++ b/modules/stxtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9ebd9c1f28e4ce3da541f707abeaa52" ] ], - "timestamp": "2026-07-28T17:05:08.497632821", + "timestamp": "2026-07-29T01:29:55.127321385", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sylph/profile/tests/main.nf.test.snap b/modules/sylph/profile/tests/main.nf.test.snap index 713b13634..62aeafd38 100644 --- a/modules/sylph/profile/tests/main.nf.test.snap +++ b/modules/sylph/profile/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-28T17:07:11.970567672", + "timestamp": "2026-07-29T01:31:58.409657025", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-28T17:06:02.478428995", + "timestamp": "2026-07-29T01:30:47.804158618", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/collate/tests/main.nf.test.snap b/modules/tbprofiler/collate/tests/main.nf.test.snap index d27931aba..b7837dead 100644 --- a/modules/tbprofiler/collate/tests/main.nf.test.snap +++ b/modules/tbprofiler/collate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,3c3d5fbb783c5cb96c154683bf56699a" ] ], - "timestamp": "2026-07-28T17:05:13.493314477", + "timestamp": "2026-07-29T01:29:58.26631694", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/profile/tests/main.nf.test.snap b/modules/tbprofiler/profile/tests/main.nf.test.snap index e4a700806..4d060180e 100644 --- a/modules/tbprofiler/profile/tests/main.nf.test.snap +++ b/modules/tbprofiler/profile/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-28T17:06:05.654435437", + "timestamp": "2026-07-29T01:30:49.127861115", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-28T17:07:00.071655149", + "timestamp": "2026-07-29T01:31:43.549826966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-28T17:08:04.874956479", + "timestamp": "2026-07-29T01:32:50.311768437", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/traitar/run/tests/main.nf.test.snap b/modules/traitar/run/tests/main.nf.test.snap index 092f218f5..311c12e58 100644 --- a/modules/traitar/run/tests/main.nf.test.snap +++ b/modules/traitar/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-28T17:11:13.940393717", + "timestamp": "2026-07-29T01:35:54.478734701", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-28T17:16:29.759672024", + "timestamp": "2026-07-29T01:41:12.495040022", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abricate/tests/main.nf.test.snap b/subworkflows/abricate/tests/main.nf.test.snap index af3e7b572..da3b3e01e 100644 --- a/subworkflows/abricate/tests/main.nf.test.snap +++ b/subworkflows/abricate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-07-28T17:05:24.089706956", + "timestamp": "2026-07-29T01:30:06.743112087", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abritamr/tests/main.nf.test.snap b/subworkflows/abritamr/tests/main.nf.test.snap index d05b4ace9..aaed94a18 100644 --- a/subworkflows/abritamr/tests/main.nf.test.snap +++ b/subworkflows/abritamr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-07-28T17:09:35.722894995", + "timestamp": "2026-07-29T01:34:15.196675503", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/agrvate/tests/main.nf.test.snap b/subworkflows/agrvate/tests/main.nf.test.snap index 060975856..bce6ff19d 100644 --- a/subworkflows/agrvate/tests/main.nf.test.snap +++ b/subworkflows/agrvate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-28T17:05:29.324054494", + "timestamp": "2026-07-29T01:30:16.45924252", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/amrfinderplus/tests/main.nf.test.snap b/subworkflows/amrfinderplus/tests/main.nf.test.snap index 0e28895a8..5b73eac55 100644 --- a/subworkflows/amrfinderplus/tests/main.nf.test.snap +++ b/subworkflows/amrfinderplus/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-07-28T17:05:38.084290058", + "timestamp": "2026-07-29T01:30:24.02145379", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ariba/tests/main.nf.test.snap b/subworkflows/ariba/tests/main.nf.test.snap index 0f5834aa1..b02ffcba9 100644 --- a/subworkflows/ariba/tests/main.nf.test.snap +++ b/subworkflows/ariba/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6" ] ], - "timestamp": "2026-07-28T17:12:37.41821209", + "timestamp": "2026-07-29T01:37:29.525427341", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap index 65f0941b3..da343ba40 100644 --- a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap +++ b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e46de3078794860a978e2dd0b390c27c" ] ], - "timestamp": "2026-07-28T17:06:50.814548918", + "timestamp": "2026-07-29T01:31:33.92428099", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bakta/tests/main.nf.test.snap b/subworkflows/bakta/tests/main.nf.test.snap index c1d34bef4..4a2892e78 100644 --- a/subworkflows/bakta/tests/main.nf.test.snap +++ b/subworkflows/bakta/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-28T17:09:33.812878779", + "timestamp": "2026-07-29T01:34:21.723312817", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastn/tests/main.nf.test.snap b/subworkflows/blastn/tests/main.nf.test.snap index 2a55326c6..2c2ca7dc2 100644 --- a/subworkflows/blastn/tests/main.nf.test.snap +++ b/subworkflows/blastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-28T17:05:44.851740724", + "timestamp": "2026-07-29T01:30:25.346784151", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastp/tests/main.nf.test.snap b/subworkflows/blastp/tests/main.nf.test.snap index 87acd319f..9cd6052f9 100644 --- a/subworkflows/blastp/tests/main.nf.test.snap +++ b/subworkflows/blastp/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-28T17:05:45.638516837", + "timestamp": "2026-07-29T01:30:33.502856524", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastx/tests/main.nf.test.snap b/subworkflows/blastx/tests/main.nf.test.snap index c3bd8b7c7..082bc4476 100644 --- a/subworkflows/blastx/tests/main.nf.test.snap +++ b/subworkflows/blastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-28T17:05:48.712350516", + "timestamp": "2026-07-29T01:30:34.326686053", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/btyper3/tests/main.nf.test.snap b/subworkflows/btyper3/tests/main.nf.test.snap index 283728ec8..8c7b6a24c 100644 --- a/subworkflows/btyper3/tests/main.nf.test.snap +++ b/subworkflows/btyper3/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-07-28T17:07:34.749578586", + "timestamp": "2026-07-29T01:32:20.254687553", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/busco/tests/main.nf.test.snap b/subworkflows/busco/tests/main.nf.test.snap index 208e9463c..87923e638 100644 --- a/subworkflows/busco/tests/main.nf.test.snap +++ b/subworkflows/busco/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-07-28T17:06:16.389757249", + "timestamp": "2026-07-29T01:31:00.588487004", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm/tests/main.nf.test.snap b/subworkflows/checkm/tests/main.nf.test.snap index 916abbaf3..925647384 100644 --- a/subworkflows/checkm/tests/main.nf.test.snap +++ b/subworkflows/checkm/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-07-28T17:08:01.285199969", + "timestamp": "2026-07-29T01:32:49.469775023", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm2/tests/main.nf.test.snap b/subworkflows/checkm2/tests/main.nf.test.snap index 5fb769251..d8708eef0 100644 --- a/subworkflows/checkm2/tests/main.nf.test.snap +++ b/subworkflows/checkm2/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-07-28T17:10:52.675813409", + "timestamp": "2026-07-29T01:35:39.175475676", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clermontyping/tests/main.nf.test.snap b/subworkflows/clermontyping/tests/main.nf.test.snap index 0649874c0..36614c5a3 100644 --- a/subworkflows/clermontyping/tests/main.nf.test.snap +++ b/subworkflows/clermontyping/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-07-28T17:06:19.527120521", + "timestamp": "2026-07-29T01:31:08.906240322", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clonalframeml/tests/main.nf.test.snap b/subworkflows/clonalframeml/tests/main.nf.test.snap index 3a9733ef1..e71e0e3dd 100644 --- a/subworkflows/clonalframeml/tests/main.nf.test.snap +++ b/subworkflows/clonalframeml/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,77f64a20eeab9152a61953ec5203b926" ] ], - "timestamp": "2026-07-28T17:07:09.542810063", + "timestamp": "2026-07-29T01:32:01.093772558", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/deacon/tests/main.nf.test.snap b/subworkflows/deacon/tests/main.nf.test.snap index b3c366c35..261708302 100644 --- a/subworkflows/deacon/tests/main.nf.test.snap +++ b/subworkflows/deacon/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,9d3e1c1b5110e0048698861366ed5151" ] ], - "timestamp": "2026-07-28T17:06:18.389528469", + "timestamp": "2026-07-29T01:31:09.405549548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/defensefinder/tests/main.nf.test.snap b/subworkflows/defensefinder/tests/main.nf.test.snap index 5cfd2b865..e37849cdb 100644 --- a/subworkflows/defensefinder/tests/main.nf.test.snap +++ b/subworkflows/defensefinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,cac1e24b64c152890e712ac2077fc111" ] ], - "timestamp": "2026-07-28T17:06:58.344177395", + "timestamp": "2026-07-29T01:31:51.41904158", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ectyper/tests/main.nf.test.snap b/subworkflows/ectyper/tests/main.nf.test.snap index c14840981..fc0a03085 100644 --- a/subworkflows/ectyper/tests/main.nf.test.snap +++ b/subworkflows/ectyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-28T17:06:31.999569833", + "timestamp": "2026-07-29T01:31:21.682749302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/eggnog/tests/main.nf.test.snap b/subworkflows/eggnog/tests/main.nf.test.snap index 7ba729caa..1fd64899c 100644 --- a/subworkflows/eggnog/tests/main.nf.test.snap +++ b/subworkflows/eggnog/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" ] ], - "timestamp": "2026-07-28T17:20:20.187785155", + "timestamp": "2026-07-29T01:45:10.522762836", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/emmtyper/tests/main.nf.test.snap b/subworkflows/emmtyper/tests/main.nf.test.snap index f391c7286..654706fb5 100644 --- a/subworkflows/emmtyper/tests/main.nf.test.snap +++ b/subworkflows/emmtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-28T17:06:14.717092187", + "timestamp": "2026-07-29T01:30:58.588619788", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/fastani/tests/main.nf.test.snap b/subworkflows/fastani/tests/main.nf.test.snap index 526856891..9e4ad8caf 100644 --- a/subworkflows/fastani/tests/main.nf.test.snap +++ b/subworkflows/fastani/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-28T17:06:15.47249014", + "timestamp": "2026-07-29T01:31:00.320189923", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gamma/tests/main.nf.test.snap b/subworkflows/gamma/tests/main.nf.test.snap index 945370a6c..40a7222d3 100644 --- a/subworkflows/gamma/tests/main.nf.test.snap +++ b/subworkflows/gamma/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-07-28T17:06:16.30177237", + "timestamp": "2026-07-29T01:31:03.007160677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genomedl/tests/main.nf.test.snap b/subworkflows/genomedl/tests/main.nf.test.snap index 40aecc613..70b3c7cec 100644 --- a/subworkflows/genomedl/tests/main.nf.test.snap +++ b/subworkflows/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-28T17:06:36.276146878", + "timestamp": "2026-07-29T01:31:22.747968011", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-28T17:06:53.898888401", + "timestamp": "2026-07-29T01:31:39.120738784", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-28T17:06:19.392094773", + "timestamp": "2026-07-29T01:31:05.511427719", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genotyphi/tests/main.nf.test.snap b/subworkflows/genotyphi/tests/main.nf.test.snap index b655f0f77..853f5f278 100644 --- a/subworkflows/genotyphi/tests/main.nf.test.snap +++ b/subworkflows/genotyphi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-07-28T17:06:31.069260965", + "timestamp": "2026-07-29T01:31:15.456870595", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gigatyper/tests/main.nf.test.snap b/subworkflows/gigatyper/tests/main.nf.test.snap index 97e52b1e2..e9064eabb 100644 --- a/subworkflows/gigatyper/tests/main.nf.test.snap +++ b/subworkflows/gigatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-28T17:06:35.919557255", + "timestamp": "2026-07-29T01:31:22.433297539", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gtdb/tests/main.nf.test.snap b/subworkflows/gtdb/tests/main.nf.test.snap index 6b352c031..4afaa9403 100644 --- a/subworkflows/gtdb/tests/main.nf.test.snap +++ b/subworkflows/gtdb/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-28T17:11:32.840424346", + "timestamp": "2026-07-29T01:36:17.045906766", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gubbins/tests/main.nf.test.snap b/subworkflows/gubbins/tests/main.nf.test.snap index 5a76fd542..6337b1197 100644 --- a/subworkflows/gubbins/tests/main.nf.test.snap +++ b/subworkflows/gubbins/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,a8d93e0d6a006b32c088567301fe66c4" ] ], - "timestamp": "2026-07-28T17:06:49.502506719", + "timestamp": "2026-07-29T01:31:33.968264893", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hicap/tests/main.nf.test.snap b/subworkflows/hicap/tests/main.nf.test.snap index 8aa20ff02..c735fc49e 100644 --- a/subworkflows/hicap/tests/main.nf.test.snap +++ b/subworkflows/hicap/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-28T17:06:54.161586632", + "timestamp": "2026-07-29T01:31:38.216821349", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hpsuissero/tests/main.nf.test.snap b/subworkflows/hpsuissero/tests/main.nf.test.snap index e71e00f91..e219538a5 100644 --- a/subworkflows/hpsuissero/tests/main.nf.test.snap +++ b/subworkflows/hpsuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-28T17:06:28.284182837", + "timestamp": "2026-07-29T01:31:17.100346315", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/iqtree/tests/main.nf.test.snap b/subworkflows/iqtree/tests/main.nf.test.snap index 8eec959ed..5cb5779a7 100644 --- a/subworkflows/iqtree/tests/main.nf.test.snap +++ b/subworkflows/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f" ] ], - "timestamp": "2026-07-28T17:06:33.455698419", + "timestamp": "2026-07-29T01:31:20.642269187", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ismapper/tests/main.nf.test.snap b/subworkflows/ismapper/tests/main.nf.test.snap index 94f8716c0..cbad8b78b 100644 --- a/subworkflows/ismapper/tests/main.nf.test.snap +++ b/subworkflows/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-28T17:07:44.514397831", + "timestamp": "2026-07-29T01:32:32.308738036", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kleborate/tests/main.nf.test.snap b/subworkflows/kleborate/tests/main.nf.test.snap index 900cf1b3a..ac77cc2ad 100644 --- a/subworkflows/kleborate/tests/main.nf.test.snap +++ b/subworkflows/kleborate/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-28T17:07:05.900039873", + "timestamp": "2026-07-29T01:31:54.671281793", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kraken2/tests/main.nf.test.snap b/subworkflows/kraken2/tests/main.nf.test.snap index e2f34b81a..b7a6702b2 100644 --- a/subworkflows/kraken2/tests/main.nf.test.snap +++ b/subworkflows/kraken2/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-28T17:07:11.030883655", + "timestamp": "2026-07-29T01:31:58.539251149", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/legsta/tests/main.nf.test.snap b/subworkflows/legsta/tests/main.nf.test.snap index 852d36f3c..f77204239 100644 --- a/subworkflows/legsta/tests/main.nf.test.snap +++ b/subworkflows/legsta/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-28T17:06:49.435996446", + "timestamp": "2026-07-29T01:31:42.192658084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/lissero/tests/main.nf.test.snap b/subworkflows/lissero/tests/main.nf.test.snap index 4c11a75b3..ba733dbc3 100644 --- a/subworkflows/lissero/tests/main.nf.test.snap +++ b/subworkflows/lissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-28T17:06:54.015665013", + "timestamp": "2026-07-29T01:31:45.264431252", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashdist/tests/main.nf.test.snap b/subworkflows/mashdist/tests/main.nf.test.snap index 206186f19..d84657ba3 100644 --- a/subworkflows/mashdist/tests/main.nf.test.snap +++ b/subworkflows/mashdist/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,fa387a5652585c181be4884eb12f37b0" ] ], - "timestamp": "2026-07-28T17:06:59.318642745", + "timestamp": "2026-07-29T01:31:43.70879255", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashtree/tests/main.nf.test.snap b/subworkflows/mashtree/tests/main.nf.test.snap index 8bf062b3b..82886928a 100644 --- a/subworkflows/mashtree/tests/main.nf.test.snap +++ b/subworkflows/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8cd0c9b6f670d5ae21fda6592e85d32" ] ], - "timestamp": "2026-07-28T17:06:59.284666206", + "timestamp": "2026-07-29T01:31:44.050773236", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mcroni/tests/main.nf.test.snap b/subworkflows/mcroni/tests/main.nf.test.snap index c8f6a067b..16625f6b1 100644 --- a/subworkflows/mcroni/tests/main.nf.test.snap +++ b/subworkflows/mcroni/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,6eecf339ecef6511e62beca33a4b3fc6" ] ], - "timestamp": "2026-07-28T17:07:03.359354314", + "timestamp": "2026-07-29T01:32:01.241013814", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/meningotype/tests/main.nf.test.snap b/subworkflows/meningotype/tests/main.nf.test.snap index 0b3b367a0..d30b986c3 100644 --- a/subworkflows/meningotype/tests/main.nf.test.snap +++ b/subworkflows/meningotype/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2210210917992673f792050a55c95b2e" ] ], - "timestamp": "2026-07-28T17:07:04.025549387", + "timestamp": "2026-07-29T01:32:06.321275068", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/merlindist/tests/main.nf.test.snap b/subworkflows/merlindist/tests/main.nf.test.snap index f47c21365..931ebb963 100644 --- a/subworkflows/merlindist/tests/main.nf.test.snap +++ b/subworkflows/merlindist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,a714676ea5e603813de6640079a3f847" ] ], - "timestamp": "2026-07-28T17:08:20.492381982", + "timestamp": "2026-07-29T01:33:13.458420293", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/midas/tests/main.nf.test.snap b/subworkflows/midas/tests/main.nf.test.snap index bdc5b75c5..4b6f778ba 100644 --- a/subworkflows/midas/tests/main.nf.test.snap +++ b/subworkflows/midas/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,66c2179f6d22e371b66b5d12ec5b0af1" ] ], - "timestamp": "2026-07-28T17:14:25.322217018", + "timestamp": "2026-07-29T01:39:16.586672957", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mlst/tests/main.nf.test.snap b/subworkflows/mlst/tests/main.nf.test.snap index 4f3991be4..e6e24d063 100644 --- a/subworkflows/mlst/tests/main.nf.test.snap +++ b/subworkflows/mlst/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-07-28T17:07:32.707561881", + "timestamp": "2026-07-29T01:32:16.372288157", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mobsuite/tests/main.nf.test.snap b/subworkflows/mobsuite/tests/main.nf.test.snap index 88623cd4b..30119da3f 100644 --- a/subworkflows/mobsuite/tests/main.nf.test.snap +++ b/subworkflows/mobsuite/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,e586a98fe29a48792ce661d2649ada18" ] ], - "timestamp": "2026-07-28T17:08:35.407292884", + "timestamp": "2026-07-29T01:33:33.310297379", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mykrobe/tests/main.nf.test.snap b/subworkflows/mykrobe/tests/main.nf.test.snap index 315c9a0cc..707dae741 100644 --- a/subworkflows/mykrobe/tests/main.nf.test.snap +++ b/subworkflows/mykrobe/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-28T17:07:32.136787338", + "timestamp": "2026-07-29T01:32:26.08276497", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ngmaster/tests/main.nf.test.snap b/subworkflows/ngmaster/tests/main.nf.test.snap index b8c9ccf66..410a35a14 100644 --- a/subworkflows/ngmaster/tests/main.nf.test.snap +++ b/subworkflows/ngmaster/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9dbc0e8b7902e955ec10c94c11074f06" ] ], - "timestamp": "2026-07-28T17:07:37.950807411", + "timestamp": "2026-07-29T01:32:34.402363664", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/nohuman/tests/main.nf.test.snap b/subworkflows/nohuman/tests/main.nf.test.snap index e19d4d6a5..594da4bc9 100644 --- a/subworkflows/nohuman/tests/main.nf.test.snap +++ b/subworkflows/nohuman/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,75d067d7ecc44ec6c90a321b8103c997" ] ], - "timestamp": "2026-07-28T17:12:19.114645996", + "timestamp": "2026-07-29T01:37:10.520038223", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/panaroo/tests/main.nf.test.snap b/subworkflows/panaroo/tests/main.nf.test.snap index b73fb5852..b7927fe59 100644 --- a/subworkflows/panaroo/tests/main.nf.test.snap +++ b/subworkflows/panaroo/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,0e38cb68a88a1a2911e751e9a8ffd648" ] ], - "timestamp": "2026-07-28T17:09:10.973777305", + "timestamp": "2026-07-29T01:34:04.286068861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pangenome/tests/main.nf.test.snap b/subworkflows/pangenome/tests/main.nf.test.snap index f9f26192b..4e0505db0 100644 --- a/subworkflows/pangenome/tests/main.nf.test.snap +++ b/subworkflows/pangenome/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T17:09:12.677207098", + "timestamp": "2026-07-29T01:34:06.316490703", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pasty/tests/main.nf.test.snap b/subworkflows/pasty/tests/main.nf.test.snap index b80d09d0c..c9ce75abc 100644 --- a/subworkflows/pasty/tests/main.nf.test.snap +++ b/subworkflows/pasty/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,d806f451289eb221f11075799712603e" ] ], - "timestamp": "2026-07-28T17:07:49.736137256", + "timestamp": "2026-07-29T01:32:36.783413869", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pbptyper/tests/main.nf.test.snap b/subworkflows/pbptyper/tests/main.nf.test.snap index 6aa951685..722e3ac8e 100644 --- a/subworkflows/pbptyper/tests/main.nf.test.snap +++ b/subworkflows/pbptyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18" ] ], - "timestamp": "2026-07-28T17:08:16.195397015", + "timestamp": "2026-07-29T01:33:07.555864876", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/phispy/tests/main.nf.test.snap b/subworkflows/phispy/tests/main.nf.test.snap index 5c699c1e4..ae79b6c6b 100644 --- a/subworkflows/phispy/tests/main.nf.test.snap +++ b/subworkflows/phispy/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-28T17:10:00.907077676", + "timestamp": "2026-07-29T01:34:50.379277628", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pirate/tests/main.nf.test.snap b/subworkflows/pirate/tests/main.nf.test.snap index 3bcbc31c4..2ef88c474 100644 --- a/subworkflows/pirate/tests/main.nf.test.snap +++ b/subworkflows/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,424257d69beae21355dee29eac16ca77" ] ], - "timestamp": "2026-07-28T17:10:36.275704573", + "timestamp": "2026-07-29T01:35:28.739823018", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/plasmidfinder/tests/main.nf.test.snap b/subworkflows/plasmidfinder/tests/main.nf.test.snap index d20f88560..2be0d92fa 100644 --- a/subworkflows/plasmidfinder/tests/main.nf.test.snap +++ b/subworkflows/plasmidfinder/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-28T17:07:55.903861211", + "timestamp": "2026-07-29T01:32:44.330042395", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pneumocat/tests/main.nf.test.snap b/subworkflows/pneumocat/tests/main.nf.test.snap index f3573f2e8..ae6ad4cc2 100644 --- a/subworkflows/pneumocat/tests/main.nf.test.snap +++ b/subworkflows/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-28T17:08:14.3721084", + "timestamp": "2026-07-29T01:33:05.586353018", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/prokka/tests/main.nf.test.snap b/subworkflows/prokka/tests/main.nf.test.snap index 06ee957a6..d8a5b0926 100644 --- a/subworkflows/prokka/tests/main.nf.test.snap +++ b/subworkflows/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-28T17:08:04.569776837", + "timestamp": "2026-07-29T01:32:59.993393914", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/quast/tests/main.nf.test.snap b/subworkflows/quast/tests/main.nf.test.snap index d321b76d6..165d66eae 100644 --- a/subworkflows/quast/tests/main.nf.test.snap +++ b/subworkflows/quast/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6625779099decc901ee6311371b1230" ] ], - "timestamp": "2026-07-28T17:08:00.903619665", + "timestamp": "2026-07-29T01:32:58.257588548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/rgi/tests/main.nf.test.snap b/subworkflows/rgi/tests/main.nf.test.snap index 23dbcdef0..1a69fe461 100644 --- a/subworkflows/rgi/tests/main.nf.test.snap +++ b/subworkflows/rgi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,c1294552ba205b057bd368875a4eac93" ] ], - "timestamp": "2026-07-28T18:35:33.791763973", + "timestamp": "2026-07-29T01:33:57.888308447", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/roary/tests/main.nf.test.snap b/subworkflows/roary/tests/main.nf.test.snap index 2a2d1f1ae..76fa02697 100644 --- a/subworkflows/roary/tests/main.nf.test.snap +++ b/subworkflows/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d5496a62b5ffe9e5af444bfc53221551" ] ], - "timestamp": "2026-07-28T17:09:14.970364044", + "timestamp": "2026-07-29T01:34:16.073320749", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sccmec/tests/main.nf.test.snap b/subworkflows/sccmec/tests/main.nf.test.snap index 37da3637d..e302037c1 100644 --- a/subworkflows/sccmec/tests/main.nf.test.snap +++ b/subworkflows/sccmec/tests/main.nf.test.snap @@ -29,7 +29,7 @@ "versions.yml:md5,c6ede7b0533855a33c127cafa29de747" ] ], - "timestamp": "2026-07-28T17:08:04.469024676", + "timestamp": "2026-07-29T01:33:09.452613063", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scoary/tests/main.nf.test.snap b/subworkflows/scoary/tests/main.nf.test.snap index 9c3adce13..f3ffb8eb5 100644 --- a/subworkflows/scoary/tests/main.nf.test.snap +++ b/subworkflows/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,36d9b366d4941f258a248bf7a31aecc7" ] ], - "timestamp": "2026-07-28T17:08:12.639645628", + "timestamp": "2026-07-29T01:33:07.73530746", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scrubber/tests/main.nf.test.snap b/subworkflows/scrubber/tests/main.nf.test.snap index 468b1ec22..87045ab49 100644 --- a/subworkflows/scrubber/tests/main.nf.test.snap +++ b/subworkflows/scrubber/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-28T17:13:10.124789088", + "timestamp": "2026-07-29T01:37:56.542651421", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-28T17:13:48.231768727", + "timestamp": "2026-07-29T01:38:37.859104087", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seqsero2/tests/main.nf.test.snap b/subworkflows/seqsero2/tests/main.nf.test.snap index 886d9d79d..9854e178f 100644 --- a/subworkflows/seqsero2/tests/main.nf.test.snap +++ b/subworkflows/seqsero2/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-28T17:08:21.120755", + "timestamp": "2026-07-29T01:33:12.95288607", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seroba/tests/main.nf.test.snap b/subworkflows/seroba/tests/main.nf.test.snap index 8808d758a..48f827599 100644 --- a/subworkflows/seroba/tests/main.nf.test.snap +++ b/subworkflows/seroba/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,4fd4f724e2f19016eff39a2b524a9007" ] ], - "timestamp": "2026-07-28T17:09:07.672344725", + "timestamp": "2026-07-29T01:34:08.925148331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigapass/tests/main.nf.test.snap b/subworkflows/shigapass/tests/main.nf.test.snap index bf9defdd4..e843f3c24 100644 --- a/subworkflows/shigapass/tests/main.nf.test.snap +++ b/subworkflows/shigapass/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f481607e2b7526fd798b2375bb3cc9c4" ] ], - "timestamp": "2026-07-28T17:08:32.362126691", + "timestamp": "2026-07-29T01:33:30.972097787", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigatyper/tests/main.nf.test.snap b/subworkflows/shigatyper/tests/main.nf.test.snap index d999d7fb3..cff538246 100644 --- a/subworkflows/shigatyper/tests/main.nf.test.snap +++ b/subworkflows/shigatyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-07-28T17:08:26.895571966", + "timestamp": "2026-07-29T01:33:27.637875945", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigeifinder/tests/main.nf.test.snap b/subworkflows/shigeifinder/tests/main.nf.test.snap index c12adc347..19d20e888 100644 --- a/subworkflows/shigeifinder/tests/main.nf.test.snap +++ b/subworkflows/shigeifinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,bb067649d1cb0b7cc78ced0baa36bf0e" ] ], - "timestamp": "2026-07-28T17:08:24.034447868", + "timestamp": "2026-07-29T01:33:25.72757409", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sistr/tests/main.nf.test.snap b/subworkflows/sistr/tests/main.nf.test.snap index 650e7a3da..5eb77cdce 100644 --- a/subworkflows/sistr/tests/main.nf.test.snap +++ b/subworkflows/sistr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-28T17:08:53.346594316", + "timestamp": "2026-07-29T01:33:49.461261903", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/core/tests/main.nf.test.snap b/subworkflows/snippy/core/tests/main.nf.test.snap index 2a8b4287d..af54c97eb 100644 --- a/subworkflows/snippy/core/tests/main.nf.test.snap +++ b/subworkflows/snippy/core/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:08:31.929234822", + "timestamp": "2026-07-29T01:33:28.402009556", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/run/tests/main.nf.test.snap b/subworkflows/snippy/run/tests/main.nf.test.snap index e3a51d5ce..13e4816ae 100644 --- a/subworkflows/snippy/run/tests/main.nf.test.snap +++ b/subworkflows/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30" ] ], - "timestamp": "2026-07-28T17:08:59.258337174", + "timestamp": "2026-07-29T01:33:56.192964016", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snpdists/tests/main.nf.test.snap b/subworkflows/snpdists/tests/main.nf.test.snap index 32765019e..5d24bb230 100644 --- a/subworkflows/snpdists/tests/main.nf.test.snap +++ b/subworkflows/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b7c9ec6305cc1637c144c82ba20a94d6" ] ], - "timestamp": "2026-07-28T17:08:34.105236475", + "timestamp": "2026-07-29T01:33:43.230896597", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/spatyper/tests/main.nf.test.snap b/subworkflows/spatyper/tests/main.nf.test.snap index 390ef7c0b..5cfad3c31 100644 --- a/subworkflows/spatyper/tests/main.nf.test.snap +++ b/subworkflows/spatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2be001b7db8743258dd915dfe57337f4" ] ], - "timestamp": "2026-07-28T17:08:45.698763094", + "timestamp": "2026-07-29T01:33:53.98024966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/srahumanscrubber/tests/main.nf.test.snap b/subworkflows/srahumanscrubber/tests/main.nf.test.snap index c0fd56be6..d675017d7 100644 --- a/subworkflows/srahumanscrubber/tests/main.nf.test.snap +++ b/subworkflows/srahumanscrubber/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,ca8ec5702526f2d59b7e3c5068c1c400" ] ], - "timestamp": "2026-07-28T17:10:21.645824392", + "timestamp": "2026-07-29T01:35:36.408683648", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ssuissero/tests/main.nf.test.snap b/subworkflows/ssuissero/tests/main.nf.test.snap index 63a8ff8b1..1b423b1d8 100644 --- a/subworkflows/ssuissero/tests/main.nf.test.snap +++ b/subworkflows/ssuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b273046b082dd70970b8f4e189aa5498" ] ], - "timestamp": "2026-07-28T17:08:50.652379608", + "timestamp": "2026-07-29T01:33:48.816895407", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphopiasccmec/tests/main.nf.test.snap b/subworkflows/staphopiasccmec/tests/main.nf.test.snap index 134110449..c0d457518 100644 --- a/subworkflows/staphopiasccmec/tests/main.nf.test.snap +++ b/subworkflows/staphopiasccmec/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f59d6534316ffe1998c60f98b212d80f" ] ], - "timestamp": "2026-07-28T17:08:50.647848823", + "timestamp": "2026-07-29T01:33:55.304626746", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphscan/tests/main.nf.test.snap b/subworkflows/staphscan/tests/main.nf.test.snap index e175eae20..1eeaf8f89 100644 --- a/subworkflows/staphscan/tests/main.nf.test.snap +++ b/subworkflows/staphscan/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b" ] ], - "timestamp": "2026-07-28T17:09:05.015272733", + "timestamp": "2026-07-29T01:34:07.256604501", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stecfinder/tests/main.nf.test.snap b/subworkflows/stecfinder/tests/main.nf.test.snap index 6a86d258d..e754d2f50 100644 --- a/subworkflows/stecfinder/tests/main.nf.test.snap +++ b/subworkflows/stecfinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,a4e0bfe59670d712011a3dc00f3abeb5" ] ], - "timestamp": "2026-07-28T17:09:02.440013767", + "timestamp": "2026-07-29T01:33:56.00198215", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stxtyper/tests/main.nf.test.snap b/subworkflows/stxtyper/tests/main.nf.test.snap index 6fa2221ce..a069132eb 100644 --- a/subworkflows/stxtyper/tests/main.nf.test.snap +++ b/subworkflows/stxtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c" ] ], - "timestamp": "2026-07-28T17:09:05.058482264", + "timestamp": "2026-07-29T01:33:57.762548904", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sylph/tests/main.nf.test.snap b/subworkflows/sylph/tests/main.nf.test.snap index 33552d9e8..209dd116d 100644 --- a/subworkflows/sylph/tests/main.nf.test.snap +++ b/subworkflows/sylph/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2a85d1cd25d2a88c77d90030e05e17cf" ] ], - "timestamp": "2026-07-28T17:10:11.454967252", + "timestamp": "2026-07-29T01:35:05.468492084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastn/tests/main.nf.test.snap b/subworkflows/tblastn/tests/main.nf.test.snap index e2b2c0d15..5d78b6da9 100644 --- a/subworkflows/tblastn/tests/main.nf.test.snap +++ b/subworkflows/tblastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,413650f494aaf14a524501ce6dc5c959" ] ], - "timestamp": "2026-07-28T17:09:01.958674812", + "timestamp": "2026-07-29T01:34:01.813740555", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastx/tests/main.nf.test.snap b/subworkflows/tblastx/tests/main.nf.test.snap index 4a9df89f4..74f300929 100644 --- a/subworkflows/tblastx/tests/main.nf.test.snap +++ b/subworkflows/tblastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8ebdf55bc992d797630ad6f81b6cbe3d" ] ], - "timestamp": "2026-07-28T17:09:06.538184913", + "timestamp": "2026-07-29T01:34:04.348134325", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tbprofiler/tests/main.nf.test.snap b/subworkflows/tbprofiler/tests/main.nf.test.snap index 8271c9036..96c057a5c 100644 --- a/subworkflows/tbprofiler/tests/main.nf.test.snap +++ b/subworkflows/tbprofiler/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-07-28T17:10:04.694119884", + "timestamp": "2026-07-29T01:35:03.889084966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/teton/tests/main.nf.test.snap b/subworkflows/teton/tests/main.nf.test.snap index dd7fd84fe..74a08e509 100644 --- a/subworkflows/teton/tests/main.nf.test.snap +++ b/subworkflows/teton/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "versions.yml:md5,7d27773f1e349726172140b0c615a73b" ] ], - "timestamp": "2026-07-28T18:48:22.978120925", + "timestamp": "2026-07-29T01:42:33.525627479", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/traitar/tests/main.nf.test b/subworkflows/traitar/tests/main.nf.test index 69cc39f30..a0e8bab61 100644 --- a/subworkflows/traitar/tests/main.nf.test +++ b/subworkflows/traitar/tests/main.nf.test @@ -26,7 +26,9 @@ nextflow_workflow { then { def sample = workflow.out.sample_outputs[0] - def run = workflow.out.run_outputs[0] + def runs = workflow.out.run_outputs + def majority = runs.find { it.meta.process_name == 'traitar-majority-concat' } + def single = runs.find { it.meta.process_name == 'traitar-single-concat' } assertAll( { assert workflow.success }, { assert workflow.out.sample_outputs != null }, @@ -34,14 +36,18 @@ nextflow_workflow { { assert snapshot( sample.meta, sample.versions, - run.meta, - run.versions + majority.meta, + majority.versions, + single.meta, + single.versions ).match() }, { assert sample.majority_tsv != null }, { assert sample.single_tsv != null }, { assert sample.results != null }, - { assert run.csv != null }, - { assert run.results != null } + { assert majority.csv != null }, + { assert majority.results != null }, + { assert single.csv != null }, + { assert single.results != null } ) } } diff --git a/subworkflows/traitar/tests/main.nf.test.snap b/subworkflows/traitar/tests/main.nf.test.snap index c4c6813bc..f39d0e955 100644 --- a/subworkflows/traitar/tests/main.nf.test.snap +++ b/subworkflows/traitar/tests/main.nf.test.snap @@ -22,9 +22,20 @@ }, [ "versions.yml:md5,0876b2d126e96f86b158fe8dddf4f05f" + ], + { + "id": "traitar-single-TRAITAR:CSVTK_CONCAT_SINGLE", + "logs_dir": "merged-results/logs/traitar-single-concat/", + "name": "traitar-single", + "output_dir": "merged-results", + "process_name": "traitar-single-concat", + "scope": "run" + }, + [ + "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-28T19:49:48.509801502", + "timestamp": "2026-07-29T01:40:06.183091617", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 58bf316ad..42d0c0f53 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -1,4 +1,764 @@ { + "Bactopia (se) - SRR2838702|portiera|illumina": { + "content": [ + 11, + [ + "SRR2838702", + "SRR2838702/main", + "SRR2838702/main/annotator", + "SRR2838702/main/annotator/prokka", + "SRR2838702/main/annotator/prokka/SRR2838702-blastdb.tar.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.faa.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.ffn.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.fna.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.fsa.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.gbk.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.gff.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.sqn.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.tbl.gz", + "SRR2838702/main/annotator/prokka/SRR2838702.tsv", + "SRR2838702/main/annotator/prokka/SRR2838702.txt", + "SRR2838702/main/annotator/prokka/logs", + "SRR2838702/main/annotator/prokka/logs/SRR2838702.err", + "SRR2838702/main/annotator/prokka/logs/SRR2838702.log", + "SRR2838702/main/annotator/prokka/logs/nf.command.begin", + "SRR2838702/main/annotator/prokka/logs/nf.command.err", + "SRR2838702/main/annotator/prokka/logs/nf.command.log", + "SRR2838702/main/annotator/prokka/logs/nf.command.out", + "SRR2838702/main/annotator/prokka/logs/nf.command.run", + "SRR2838702/main/annotator/prokka/logs/nf.command.sh", + "SRR2838702/main/annotator/prokka/logs/nf.command.trace", + "SRR2838702/main/annotator/prokka/logs/versions.yml", + "SRR2838702/main/assembler", + "SRR2838702/main/assembler/SRR2838702.fna.gz", + "SRR2838702/main/assembler/SRR2838702.tsv", + "SRR2838702/main/assembler/logs", + "SRR2838702/main/assembler/logs/nf.command.begin", + "SRR2838702/main/assembler/logs/nf.command.err", + 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b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap index ebd9b6c91..4a6e2d4a3 100644 --- a/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap @@ -52,7 +52,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-07-28T17:10:43.990646647", + "timestamp": "2026-07-29T01:35:46.863782347", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap index 8dad73e3a..5bc9bd230 100644 --- a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap @@ -49,7 +49,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-28T17:09:27.619314191", + "timestamp": "2026-07-29T01:34:31.648372302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -105,7 +105,7 @@ 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a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap index d4c261861..cf27b8606 100644 --- a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap @@ -65,7 +65,7 @@ "versions.yml:md5,1a4d97856cb563f9b6c84132cd60d481" ] ], - "timestamp": "2026-07-28T17:10:00.820155818", + "timestamp": "2026-07-29T01:35:10.905627768", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap index 2e09ddbd2..68b725223 100644 --- a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-28T17:15:29.238808001", + "timestamp": "2026-07-29T01:40:35.770494544", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ 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a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap index f0e52003d..731fb9e79 100644 --- a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap @@ -66,7 +66,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-07-28T17:11:24.979774922", + "timestamp": "2026-07-29T01:36:39.195214968", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/busco/tests/main.nf.test.snap b/workflows/bactopia-tools/busco/tests/main.nf.test.snap index f1b854d5f..f4e4c0921 100644 --- a/workflows/bactopia-tools/busco/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/busco/tests/main.nf.test.snap @@ -287,7 +287,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-07-28T17:10:11.725007797", + "timestamp": "2026-07-29T01:35:22.004804379", "meta": { "nf-test": "0.9.5", "nextflow": 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"0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap index 9f1bace01..5a306bab1 100644 --- a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-07-28T17:10:27.878994436", + "timestamp": "2026-07-29T01:35:36.782116658", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap index 18dd35eb6..41ab5211d 100644 --- a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap @@ -70,7 +70,7 @@ "versions.yml:md5,cb06109c537fb7ff30a68b0a1197889d" ] ], - "timestamp": "2026-07-28T17:10:35.918111152", + "timestamp": "2026-07-29T01:35:43.135763767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap index fbf3090c7..48dad5979 100644 --- a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-28T17:10:28.709123296", + "timestamp": "2026-07-29T01:35:38.998880103", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap index 2107ac112..ea2db0fb2 100644 --- a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap @@ -29,7 +29,7 @@ "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" ] ], - "timestamp": "2026-07-28T17:15:30.347312097", + "timestamp": "2026-07-29T01:40:37.864411574", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap index 26e5022cc..5a88de87f 100644 --- a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-28T17:10:08.616467306", + "timestamp": "2026-07-29T01:35:26.657973043", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-28T17:10:38.932643181", + "timestamp": "2026-07-29T01:35:57.257668202", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap index 82cf44096..83dd2ba43 100644 --- a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap @@ -38,7 +38,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-28T17:11:17.785171064", + "timestamp": "2026-07-29T01:36:32.656876257", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-28T17:10:38.958691222", + "timestamp": "2026-07-29T01:35:57.376555197", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-28T17:10:08.854942179", + "timestamp": "2026-07-29T01:35:26.397700434", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap index 338f3e2af..fb99a565d 100644 --- a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-07-28T17:10:14.160012766", + "timestamp": "2026-07-29T01:35:31.742700745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap index be33cd3c8..6bba5e9a6 100644 --- a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap @@ -57,7 +57,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-07-28T17:10:27.912243816", + "timestamp": "2026-07-29T01:35:39.51924813", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap index 675dc1528..ea2965f88 100644 --- a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-28T17:10:39.152280841", + "timestamp": "2026-07-29T01:36:03.090230544", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap index 986416e75..956ba75ec 100644 --- a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap @@ -47,7 +47,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-28T17:15:04.781787076", + "timestamp": "2026-07-29T01:40:19.298577757", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap index e023c3bd5..634fd48ec 100644 --- a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap @@ -61,7 +61,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-28T17:11:07.695051593", + "timestamp": "2026-07-29T01:36:16.965061126", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap index 2234a836a..881c87a87 100644 --- a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-28T17:10:45.440012805", + "timestamp": "2026-07-29T01:36:06.775856956", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap index 958df9149..2467ec2ae 100644 --- a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap @@ -1068,7 +1068,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-28T17:11:43.593358144", + "timestamp": "2026-07-29T01:36:56.157718753", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap index d463d6cb6..fe6a2f397 100644 --- a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-28T17:11:29.984572514", + "timestamp": "2026-07-29T01:37:00.813038011", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap index e733d9a0c..b621ba5d2 100644 --- a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-28T17:14:20.333481913", + "timestamp": "2026-07-29T01:41:29.129678843", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -63,7 +63,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-28T17:15:00.893027942", + "timestamp": "2026-07-29T01:41:59.441065364", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap index 8527d964a..d0c26cd62 100644 --- a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-28T17:11:29.082997324", + "timestamp": "2026-07-29T01:36:39.097407223", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap index e4a210acb..df1e4240e 100644 --- a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-28T17:11:31.456913119", + "timestamp": "2026-07-29T01:36:38.262569677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap index 722b48841..525105f43 100644 --- a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap @@ -43,7 +43,7 @@ "mashdist.tsv:md5,630500729ddf987a8f487cd409d0afce" ] ], - "timestamp": "2026-07-28T17:11:35.231047777", + "timestamp": "2026-07-29T01:36:42.094510609", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap index 1866ccc0f..c7ef3c62e 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "mashtree.dnd:md5,2b2d08b0bf16e25717f5db0eca6eba6b" ] ], - "timestamp": "2026-07-28T17:11:37.241906731", + "timestamp": "2026-07-29T01:36:43.913834134", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "mashtree.dnd:md5,02f89fd1a5f4a3a92df0b016061f67dd" ] ], - "timestamp": "2026-07-28T17:12:06.423579656", + "timestamp": "2026-07-29T01:37:13.049369818", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap index e6148e902..09e55cd95 100644 --- a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "mcroni.tsv:md5,c5459d2965dfafe22f173023d0c35610" ] ], - "timestamp": "2026-07-28T17:11:44.024513745", + "timestamp": "2026-07-29T01:36:49.896482144", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap index 92b4b2ec0..8e68ebcd8 100644 --- a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "meningotype.tsv:md5,cdf1cbd9f28a9ce2138f072c6d0ab391" ] ], - "timestamp": "2026-07-28T17:11:44.713911402", + "timestamp": "2026-07-29T01:36:49.846022063", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap index f97f190ca..7934782c7 100644 --- a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap @@ -386,7 +386,7 @@ ] ], - "timestamp": "2026-07-28T17:13:34.747448959", + "timestamp": "2026-07-29T01:38:36.700683413", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -973,7 +973,7 @@ ] ], - "timestamp": "2026-07-28T17:15:25.362968386", + "timestamp": "2026-07-29T01:40:27.32965059", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/midas/tests/main.nf.test.snap b/workflows/bactopia-tools/midas/tests/main.nf.test.snap index 9d36f4277..c56951f3f 100644 --- a/workflows/bactopia-tools/midas/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/midas/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-28T17:12:30.355218637", + "timestamp": "2026-07-29T01:37:29.568331075", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -99,7 +99,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-28T17:13:34.746758901", + "timestamp": "2026-07-29T01:38:33.559499623", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap index 54882f160..a2efc40b7 100644 --- a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "mlst.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6" ] ], - "timestamp": "2026-07-28T17:11:59.576599362", + "timestamp": "2026-07-29T01:36:57.602958653", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap index 0c0419735..41d0d8e05 100644 --- a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "mobsuite.tsv:md5,951dbd706ab78c4d00aa28735ab34e87" ] ], - "timestamp": "2026-07-28T17:12:34.151817352", + "timestamp": "2026-07-29T01:37:39.525998546", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap index 7c089150d..9e1f75e25 100644 --- a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap @@ -41,7 +41,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-28T17:11:58.029504474", + "timestamp": "2026-07-29T01:37:03.270460416", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap index 523f5286c..64598556c 100644 --- a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ngmaster.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219" ] ], - "timestamp": "2026-07-28T17:12:06.096077734", + "timestamp": "2026-07-29T01:37:09.555667277", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap index 73969655c..469dec85b 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap @@ -140,7 +140,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:08:29.948976259", + "timestamp": "2026-07-29T01:44:38.676764579", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -314,7 +314,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:06:33.807080285", + "timestamp": "2026-07-29T01:42:19.838411501", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -447,7 +447,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:07:31.819117432", + "timestamp": "2026-07-29T01:43:31.086283461", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -579,7 +579,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:03:47.313952314", + "timestamp": "2026-07-29T01:38:38.008748726", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -663,7 +663,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:04:27.323618465", + "timestamp": "2026-07-29T01:39:42.265173667", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -747,7 +747,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-28T20:05:19.973058681", + "timestamp": "2026-07-29T01:40:54.197027582", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap index f6a3f66d5..63283d5f0 100644 --- a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "pasty.tsv:md5,3f0b647b733d1c01212c1f475527aef4" ] ], - "timestamp": "2026-07-28T17:12:08.300371346", + "timestamp": "2026-07-29T01:37:15.05939135", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap index c7cd5dc47..668966885 100644 --- a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "pbptyper.tsv:md5,34edc1f9346b74b74ef4446d270e6d57" ] ], - "timestamp": "2026-07-28T17:12:43.010445622", + "timestamp": "2026-07-29T01:37:53.634175779", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap index 8a4cee6a2..e99d2b607 100644 --- a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap @@ -60,7 +60,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-28T17:12:55.882689995", + "timestamp": "2026-07-29T01:38:16.712434613", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap index 1fc2ebf9e..5933c5fdc 100644 --- a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-28T17:12:17.278174521", + "timestamp": "2026-07-29T01:37:25.026660028", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap index e75ba67c5..4d820228b 100644 --- a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-28T17:12:19.823973883", + "timestamp": "2026-07-29T01:37:25.257893434", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap index 30941ef56..8902df7e4 100644 --- a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-28T17:12:30.648349748", + "timestamp": "2026-07-29T01:37:39.540498378", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/quast/tests/main.nf.test.snap b/workflows/bactopia-tools/quast/tests/main.nf.test.snap index 673f07bbc..2a0f3540e 100644 --- a/workflows/bactopia-tools/quast/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/quast/tests/main.nf.test.snap @@ -69,7 +69,7 @@ "quast.tsv:md5,a02f798379d9982810a198ec9b389079" ] ], - "timestamp": "2026-07-28T17:12:37.761771394", + "timestamp": "2026-07-29T01:37:40.847741354", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap index 1d1a234ef..53a4b0693 100644 --- a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap @@ -76,7 +76,7 @@ "versions.yml:md5,69941ec700f55e09c1a930ed36f54b0c" ] ], - "timestamp": "2026-07-28T18:33:45.287947145", + "timestamp": "2026-07-29T01:38:37.072072086", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap index dd84b7f4a..c3d91fa39 100644 --- a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap @@ -50,7 +50,7 @@ "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" ] ], - "timestamp": "2026-07-28T17:13:13.950341218", + "timestamp": "2026-07-29T01:38:24.795826641", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -107,7 +107,7 @@ "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" ] ], - "timestamp": "2026-07-28T17:12:37.38061554", + "timestamp": "2026-07-29T01:37:42.751129903", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap index 93d281edc..69d5edbbd 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "scrubber.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d" ] ], - "timestamp": "2026-07-28T17:12:47.592328778", + "timestamp": "2026-07-29T01:37:56.966328894", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -96,7 +96,7 @@ "scrubber.tsv:md5,e957775ff85716621f5fdd536de5b417" ] ], - "timestamp": "2026-07-28T17:17:02.76227411", + "timestamp": "2026-07-29T01:42:14.657285073", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "scrubber.tsv:md5,9554a4a6929bbfd485e28acd4a716772" ] ], - "timestamp": "2026-07-28T17:17:57.711891391", + "timestamp": "2026-07-29T01:43:05.742795155", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap index f8913cc21..bed78f482 100644 --- a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-28T17:12:37.848465503", + "timestamp": "2026-07-29T01:37:40.798731672", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap index ea6cb3475..e33ff9a08 100644 --- a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "seroba.tsv:md5,8c20690cc5ca0fd77228c830001e0b86" ] ], - "timestamp": "2026-07-28T17:13:10.815719428", + "timestamp": "2026-07-29T01:38:21.84953609", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap index 92ce774b8..edb8ea411 100644 --- a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "shigapass.tsv:md5,9982dbc252423a0507b7c397f66164f2" ] ], - "timestamp": "2026-07-28T17:12:49.478347629", + "timestamp": "2026-07-29T01:37:50.673257637", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap index 73f4c3dd5..fbe9db514 100644 --- a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap @@ -78,7 +78,7 @@ "shigatyper.tsv:md5,6041948e454daeabef20a6f725047dca" ] ], - "timestamp": "2026-07-28T17:12:44.466999633", + "timestamp": "2026-07-29T01:37:46.020804099", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap index dc5775a46..6027dab5a 100644 --- a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "shigeifinder.tsv:md5,25be6cf1161e59d9a4eab8db8f9b9ebb" ] ], - "timestamp": "2026-07-28T17:12:47.76154099", + "timestamp": "2026-07-29T01:37:46.625248927", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap index b59215e7b..af8750541 100644 --- a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-28T17:13:17.569264055", + "timestamp": "2026-07-29T01:38:21.809046788", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap index c1d8dbb15..a3dcf6147 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap @@ -316,7 +316,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:13:59.293503099", + "timestamp": "2026-07-29T01:38:51.3690779", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -639,7 +639,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:15:06.651723264", + "timestamp": "2026-07-29T01:39:52.470621415", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -949,7 +949,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:16:01.437051468", + "timestamp": "2026-07-29T01:40:45.876567548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1238,7 +1238,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:17:39.155144399", + "timestamp": "2026-07-29T01:42:28.314573246", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1561,7 +1561,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:16:56.477900542", + "timestamp": "2026-07-29T01:41:44.586722915", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1850,7 +1850,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-28T17:18:27.063251165", + "timestamp": "2026-07-29T01:43:20.26633868", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap index 28ad5204b..03b616362 100644 --- a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-07-28T17:13:43.063262582", + "timestamp": "2026-07-29T01:38:45.758229414", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-07-28T17:13:14.025244723", + "timestamp": "2026-07-29T01:38:18.989677953", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap index 940637fff..7c75bfa69 100644 --- a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ssuissero.tsv:md5,b1312d3041a6543154be554d5ec3b0b9" ] ], - "timestamp": "2026-07-28T17:13:10.156993552", + "timestamp": "2026-07-29T01:38:10.866882643", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap index be845985f..a7e4c5d9d 100644 --- a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "staphscan.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e" ] ], - "timestamp": "2026-07-28T17:13:29.892080708", + "timestamp": "2026-07-29T01:38:27.243648178", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap index 0169e3493..f145cb390 100644 --- a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap @@ -132,7 +132,7 @@ "staphscan.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e" ] ], - "timestamp": "2026-07-28T17:13:34.568119151", + "timestamp": "2026-07-29T01:38:27.622765241", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap index 7883e80f5..42abd8337 100644 --- a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap @@ -72,7 +72,7 @@ "stecfinder.tsv:md5,d2b6d9a9ab37d918c58b4e8272e6055d" ] ], - "timestamp": "2026-07-28T17:13:23.504001293", + "timestamp": "2026-07-29T01:38:33.84272739", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap index 6236d0091..c3fe3a250 100644 --- a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "stxtyper.tsv:md5,99f9ffe60fe519d684ee7943641022d2" ] ], - "timestamp": "2026-07-28T17:13:29.110420034", + "timestamp": "2026-07-29T01:38:35.338512059", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap index 024a25769..0d68c8c8c 100644 --- a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "sylph.tsv:md5,beb99cbcea3c9c0a90329ae09ee957f3" ] ], - "timestamp": "2026-07-28T17:14:10.754008226", + "timestamp": "2026-07-29T01:39:20.727418276", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap index b0054cdb3..8fc3da1d3 100644 --- a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-28T17:13:27.965097802", + "timestamp": "2026-07-29T01:38:35.493868294", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-28T17:13:50.244084431", + "timestamp": "2026-07-29T01:38:58.6249142", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap index be5d51878..942098087 100644 --- a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-28T17:13:34.466516621", + "timestamp": "2026-07-29T01:38:37.053076265", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-28T17:14:14.607756685", + "timestamp": "2026-07-29T01:39:22.712807122", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "tblastx.tsv:md5,4efa1d2d8633246603e06df64e559c4c" ] ], - "timestamp": "2026-07-28T17:13:56.338698945", + "timestamp": "2026-07-29T01:39:03.537385195", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap index 9ddb63927..dbabcf818 100644 --- a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-07-28T17:14:01.47336561", + "timestamp": "2026-07-29T01:39:09.110218015", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap index cfd48de17..0f1572bba 100644 --- a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-28T17:17:36.679585092", + "timestamp": "2026-07-29T01:42:43.280691904", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/cleanyerreads/tests/main.nf.test.snap b/workflows/cleanyerreads/tests/main.nf.test.snap index 9a95b2638..dbc933968 100644 --- a/workflows/cleanyerreads/tests/main.nf.test.snap +++ b/workflows/cleanyerreads/tests/main.nf.test.snap @@ -87,7 +87,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-28T17:15:58.316832451", + "timestamp": "2026-07-29T01:40:58.602321074", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -163,7 +163,7 @@ "versions.yml:md5,61924107a406c136f55c445d470721f7" ] ], - "timestamp": "2026-07-28T17:14:35.365789194", + "timestamp": "2026-07-29T01:39:40.987158505", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/staphopia/tests/main.nf.test.snap b/workflows/staphopia/tests/main.nf.test.snap index f67f5e8ee..171aea251 100644 --- a/workflows/staphopia/tests/main.nf.test.snap +++ b/workflows/staphopia/tests/main.nf.test.snap @@ -289,7 +289,7 @@ "versions.yml:md5,c707d4291d068c2b150937480568d0b0" ] ], - "timestamp": "2026-07-28T17:18:23.171217804", + "timestamp": "2026-07-29T01:43:09.961549011", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/teton/tests/main.nf.test.snap b/workflows/teton/tests/main.nf.test.snap index 10e331af5..31efd2667 100644 --- a/workflows/teton/tests/main.nf.test.snap +++ b/workflows/teton/tests/main.nf.test.snap @@ -181,7 +181,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-07-28T17:18:44.389172726", + "timestamp": "2026-07-29T01:42:35.103899724", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -368,7 +368,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-07-28T17:28:45.981302767", + "timestamp": "2026-07-29T01:52:19.727815772", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -555,7 +555,7 @@ "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" ] ], - "timestamp": "2026-07-28T17:23:34.852640834", + "timestamp": "2026-07-29T01:47:11.054654393", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From c24b2f1866e1253d7303e4fcbdfbf5072fd9d825 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Wed, 29 Jul 2026 19:17:15 +0200 Subject: [PATCH 28/43] set NUMBA_CACHE_DIR for gubbins (#669) * Set NUMBA_CACHE_DIR to a writeable location for gubbins * Replace NUMBA_CACHE_DIR location * Replace NUMBA_CACHE_DIR location again * Replace NUMBA_CACHE_DIR location once again * use within process tmp dir for numba_cache --------- Co-authored-by: Robert A. Petit III --- modules/gubbins/main.nf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf index 5517ca9f6..f724199a5 100644 --- a/modules/gubbins/main.nf +++ b/modules/gubbins/main.nf @@ -75,6 +75,9 @@ process GUBBINS { def is_compressed = aln.getName().endsWith(".gz") ? true : false def aln_name = aln.getName().replace(".gz", "") """ + mkdir -p tmp/numba_cache + export NUMBA_CACHE_DIR="./tmp/numba_cache" + if [ "${is_compressed}" == "true" ]; then gzip -c -d ${aln} > ${aln_name} fi @@ -95,6 +98,7 @@ process GUBBINS { if [ "${is_compressed}" == "true" ]; then rm -rf ${aln_name} fi + rm -rf tmp/ gzip *.masked.aln *.embl *.fasta *.gff *.vcf # Move supplemental outputs to gubbins folder From 25137ee11f74306d9fb0c0d81db0bfbd2f180435 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 29 Jul 2026 11:54:14 -0600 Subject: [PATCH 29/43] move gubbins cleanup stepo for numba cache --- modules/gubbins/main.nf | 4 +++- modules/gubbins/tests/main.nf.test.snap | 4 ++-- modules/snippy/core/tests/main.nf.test.snap | 2 +- modules/snippy/run/tests/main.nf.test.snap | 4 ++-- subworkflows/gubbins/tests/main.nf.test.snap | 2 +- subworkflows/snippy/core/tests/main.nf.test.snap | 2 +- subworkflows/snippy/run/tests/main.nf.test.snap | 2 +- .../bactopia-tools/snippy/tests/main.nf.test.snap | 12 ++++++------ 8 files changed, 17 insertions(+), 15 deletions(-) diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf index f724199a5..4243950d9 100644 --- a/modules/gubbins/main.nf +++ b/modules/gubbins/main.nf @@ -98,7 +98,6 @@ process GUBBINS { if [ "${is_compressed}" == "true" ]; then rm -rf ${aln_name} fi - rm -rf tmp/ gzip *.masked.aln *.embl *.fasta *.gff *.vcf # Move supplemental outputs to gubbins folder @@ -118,5 +117,8 @@ process GUBBINS { "${task.process}": gubbins: \$(run_gubbins.py --version 2>&1) END_VERSIONS + + # gubbins --version causes numba cache to be recreated, so cleanup after version check + rm -rf tmp/ """ } diff --git a/modules/gubbins/tests/main.nf.test.snap b/modules/gubbins/tests/main.nf.test.snap index dfc575fa0..01057c710 100644 --- a/modules/gubbins/tests/main.nf.test.snap +++ b/modules/gubbins/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-07-29T01:28:44.679935189", + "timestamp": "2026-07-29T11:30:36.102332079", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,623c400503380dab143c222d825e55f6" ] ], - "timestamp": "2026-07-29T01:29:19.396599431", + "timestamp": "2026-07-29T11:31:06.432688377", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/core/tests/main.nf.test.snap b/modules/snippy/core/tests/main.nf.test.snap index 2650ad6cc..104ab9120 100644 --- a/modules/snippy/core/tests/main.nf.test.snap +++ b/modules/snippy/core/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,af05caa4daa181fbe9d7bf82d3383d93" ] ], - "timestamp": "2026-07-29T01:29:37.074346963", + "timestamp": "2026-07-29T11:32:47.889364457", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/run/tests/main.nf.test.snap b/modules/snippy/run/tests/main.nf.test.snap index ab632c1a6..0a03b79de 100644 --- a/modules/snippy/run/tests/main.nf.test.snap +++ b/modules/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-29T01:30:41.279350699", + "timestamp": "2026-07-29T11:33:22.643578596", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-29T01:30:02.591273048", + "timestamp": "2026-07-29T11:33:02.588615911", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gubbins/tests/main.nf.test.snap b/subworkflows/gubbins/tests/main.nf.test.snap index 6337b1197..7716e9b63 100644 --- a/subworkflows/gubbins/tests/main.nf.test.snap +++ b/subworkflows/gubbins/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,a8d93e0d6a006b32c088567301fe66c4" ] ], - "timestamp": "2026-07-29T01:31:33.968264893", + "timestamp": "2026-07-29T11:30:36.911261125", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/core/tests/main.nf.test.snap b/subworkflows/snippy/core/tests/main.nf.test.snap index af54c97eb..b24bf7a44 100644 --- a/subworkflows/snippy/core/tests/main.nf.test.snap +++ b/subworkflows/snippy/core/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:33:28.402009556", + "timestamp": "2026-07-29T11:32:49.156063798", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/run/tests/main.nf.test.snap b/subworkflows/snippy/run/tests/main.nf.test.snap index 13e4816ae..717e1231d 100644 --- a/subworkflows/snippy/run/tests/main.nf.test.snap +++ b/subworkflows/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30" ] ], - "timestamp": "2026-07-29T01:33:56.192964016", + "timestamp": "2026-07-29T11:33:05.322847047", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap index a3dcf6147..15755bf53 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap @@ -316,7 +316,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:38:51.3690779", + "timestamp": "2026-07-29T11:33:41.235800414", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -639,7 +639,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:39:52.470621415", + "timestamp": "2026-07-29T11:34:40.096134031", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -949,7 +949,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:40:45.876567548", + "timestamp": "2026-07-29T11:35:28.678459692", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1238,7 +1238,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:42:28.314573246", + "timestamp": "2026-07-29T11:37:05.876645538", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1561,7 +1561,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:41:44.586722915", + "timestamp": "2026-07-29T11:36:27.029816169", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1850,7 +1850,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T01:43:20.26633868", + "timestamp": "2026-07-29T11:37:48.147294697", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 4636904611d97274b0a7258712dccd8ae91c1b48 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 29 Jul 2026 11:58:39 -0600 Subject: [PATCH 30/43] update change log --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 66927efb2..ae2db5a4d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -72,6 +72,7 @@ sidebar_position: 5000 - `rgi` failing with `unrecognized arguments: --num_threads` after the 6.0.8 bump (renamed to `--threads`) - `rgi_exclude_nudge` emitting the removed `--exclude_nudge` flag; replaced with `rgi_include_nudge` which passes RGI 6's opt-in `--include_nudge` - `bactopia datasets` tests requesting a version-pinned `mlst.tar.gz` (404); `mlst_url` has been version-less since v4.0.0 +- `gubbins` failing under Singularity/Apptainer when Numba tried to write to read-only container ([#667](https://github.com/bactopia/bactopia/issues/667)) (@pvanheus) ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 From 1f7b6fe9843e6a5ee6972795cdf966e5ef1b6deb Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 29 Jul 2026 23:45:58 -0600 Subject: [PATCH 31/43] start test updates to include conda and singularity, not just docker --- .claude/skills/review-tests/SKILL.md | 240 ++++++++++++------ conf/params.config | 4 +- conf/test.config | 5 +- conf/test_base.config | 6 +- modules/bactopia/assembler/tests/main.nf.test | 64 +++-- modules/bactopia/qc/tests/main.nf.test | 40 +-- modules/bracken/tests/main.nf.test | 24 +- modules/eggnog/mapper/tests/main.nf.test | 16 +- modules/gubbins/tests/main.nf.test | 16 +- modules/pasty/tests/main.nf.test | 12 +- modules/pasty/tests/main.nf.test.snap | 9 +- modules/pbptyper/tests/main.nf.test | 12 +- modules/pbptyper/tests/main.nf.test.snap | 8 +- modules/quast/tests/main.nf.test | 24 +- modules/sccmec/tests/main.nf.test | 28 +- modules/sccmec/tests/main.nf.test.snap | 20 +- modules/sistr/tests/main.nf.test.snap | 4 +- subworkflows/eggnog/tests/main.nf.test | 6 +- subworkflows/gubbins/tests/main.nf.test | 4 +- subworkflows/pasty/tests/main.nf.test | 10 +- subworkflows/pasty/tests/main.nf.test.snap | 7 +- subworkflows/pbptyper/tests/main.nf.test | 8 +- subworkflows/pbptyper/tests/main.nf.test.snap | 6 +- subworkflows/quast/tests/main.nf.test | 4 +- subworkflows/sccmec/tests/main.nf.test | 12 +- subworkflows/sccmec/tests/main.nf.test.snap | 8 +- subworkflows/sistr/tests/main.nf.test.snap | 2 +- subworkflows/teton/tests/main.nf.test | 6 +- tests/.nftignore | 2 +- .../bactopia-tools/bracken/tests/.nftignore | 4 + .../bactopia-tools/eggnog/tests/.nftignore | 1 + .../bactopia-tools/pasty/tests/.nftignore | 2 + .../pasty/tests/main.nf.test.snap | 9 +- .../bactopia-tools/pbptyper/tests/.nftignore | 2 + .../pbptyper/tests/main.nf.test.snap | 8 +- .../bactopia-tools/quast/tests/.nftignore | 2 + .../bactopia-tools/sccmec/tests/.nftignore | 2 + .../sccmec/tests/main.nf.test.snap | 22 +- .../shigatyper/tests/.nftignore | 2 + .../sistr/tests/main.nf.test.snap | 2 +- .../bactopia-tools/snippy/tests/.nftignore | 1 + .../staphtyper/tests/.nftignore | 2 + .../stecfinder/tests/.nftignore | 2 + workflows/cleanyerreads/tests/.nftignore | 2 +- workflows/staphopia/tests/.nftignore | 2 +- workflows/teton/tests/.nftignore | 2 +- 46 files changed, 399 insertions(+), 275 deletions(-) diff --git a/.claude/skills/review-tests/SKILL.md b/.claude/skills/review-tests/SKILL.md index e0ebc585e..ec5b0ca5a 100644 --- a/.claude/skills/review-tests/SKILL.md +++ b/.claude/skills/review-tests/SKILL.md @@ -1,12 +1,17 @@ --- name: review-tests -description: Review nf-test run results and present a diagnostic summary with grouped error analysis. Use when asked to review tests, check test results, show test failures, analyze test output, investigate why tests failed, see what's broken, or check test status. Accepts an optional timestamp argument to review a specific run. +description: Review nf-test run results and present a diagnostic summary with grouped error analysis. Use when asked to review tests, check test results, show test failures, analyze test output, investigate why tests failed, see what's broken, or check test status. Runs are multi-profile (docker/conda/singularity) with docker as the reference baseline. Accepts an optional timestamp argument to review a specific run. --- # Review Tests Run the review-tests CLI and present the results to the user. +Runs are **multi-profile**: each component/tier is tested across up to four profiles +-- `docker` (the reference baseline), `conda`, `singularity_galaxy`, `singularity_pull`. +A cell is one (component, tier, profile). Most interpretation is a comparison of each +profile against docker. + ## Steps 1. Run `bactopia-review-tests` via the wrapper script using the **default text output** @@ -17,77 +22,154 @@ Run the review-tests CLI and present the results to the user. If the user provided a timestamp argument (e.g., `/review-tests 20260324_081306`), add `--run 20260324_081306`. -2. Present the text output directly to the user. The CLI already produces a clean, - well-formatted summary with tables. Do NOT parse JSON or write extra code to - reformat -- just relay the output with your interpretation. - -3. Add interpretation and context after showing the output: - - For **assertion_failure** results, check the run parameters shown in the output: - - If `generate` was **true**: snapshots were regenerated and the test was run a - second time against them. These are **real failures** -- the workflow output - does not match its own freshly-generated snapshot, meaning the output is - non-deterministic or the test assertions are wrong. Flag these as needing - investigation, NOT snapshot regeneration. - - If `generate` was **false** (or not shown): snapshots may be stale. - Note these likely need snapshot regeneration or investigation. - - For **undeclared_outputs** results: these are files the tool produced in its - work directory that are NOT declared in the module's `results`, `logs`, - `versions`, or `nf_logs` output fields. Present each affected module with - its undeclared file list (from the `.outputs.txt` log file). For each file, - help the user decide: - - **Add to `results`**: if the file is a real tool output users would want - (e.g., a report, summary, or data file) - - **Add to `logs`**: if the file is stderr/stdout from the tool itself - - **Add to `.outputs-ignore`**: if the file is a staging artifact, - intermediate, version-info side effect, or database file that should - not be published - The `.outputs-ignore` file lives at `modules/{name}/tests/.outputs-ignore` - with one glob pattern per line (`#` comments, blank lines allowed). - The `staging/**` directory is already ignored by default. - - For **suspiciously fast tests**: note these likely exited early without running. - - Summarize actionable items and suggested next steps. +2. Present the text output directly to the user. The CLI produces a clean summary with a + **"Status Breakdown by Profile"** matrix and one section per failing status. Do NOT + parse JSON or write extra code to reformat -- just relay the output with your interpretation. + +3. Add interpretation and context after showing the output. Interpret **by status** + (see the status reference below), and always frame failures as "which profiles differ + from docker, and why." Summarize actionable items and next steps. 4. If the text output is too large for a single response, summarize the key sections - (overview, status breakdown, failures) and note that timing details are available - on request. Use `--json` only as a fallback if the text output cannot be displayed. + (overview, status-by-profile matrix, failures) and note that per-file detail is in + `summary.json`. Use `--json`/`--pretty` or read `summary.json` directly for structured detail. + +## Status reference (per-cell `status`) + +- **`passed`** -- cell matched the committed snapshot / assertions. +- **`version_drift` / `output_drift` / `version+output_drift`** -- this profile's outputs differ + from docker: `version_drift` = `versions.yml` (runtime resolved a different tool version than the + docker container pin), `output_drift` = tool output file(s), `version+output_drift` = both. + `reason` names the divergent fields. When **docker passed** and only conda/singularity drift, this + is **genuine dependency-solve divergence**, not a bug. Fix = the **sccmec-pattern test migration** + (md5 the profile-stable files, existence-check the divergent ones, `versions` -> `contains('')`) + -- **NOT** snapshot regeneration. See `files[]` / `suggested_edit` in `summary.json` for the exact + bucketing. (A pure `version_drift` may instead warrant updating the container version pin.) +- **`snapshot_mismatch`** -- the snapshot didn't match but the files matrix could not attribute it to + specific fields (drift not subclassified). Inspect `files[]` and `{profile}/stderr.txt`. +- **`snapshot_stale`** -- the committed `.snap` no longer matches the **reference runtime (docker)**; + it shows on **all profiles including docker**. Fix: re-run with `--generate` under docker to + re-baseline. NOT a content or tool problem (on `generate=false`, docker's own mismatch is promoted + to this). Typical cause: a test's `snapshot()` shape was edited but `.snap` was never regenerated. +- **`assertion_failed`** -- a non-snapshot assertion failed (no output divergence detected). A test + logic/assertion issue, not drift -- read `{profile}/stderr.txt`. +- **`non_reproducible`** -- two docker runs produced different snapshots; docker's own output is + non-deterministic. Investigate the tool/test; regeneration will not fix it. +- **`build_failed`** -- the Conda env or Singularity image failed to build before testing. Infra: + build the env/image, then re-run (it blocks triage of that profile). +- **`no_ground_truth`** -- docker established no snapshot for the non-docker profiles to validate + against (usually docker itself failed to produce one). +- **`syntax_error`** -- the Nextflow script failed to compile. Fix the `.nf`. +- Housekeeping statuses you may also see: `skipped`, `timeout` (exceeded the per-run timeout), + `no_snapshot`, `n/a`. +- **`undeclared_outputs`** -- the tool produced files not declared in the module's `results`, + `logs`, `versions`, or `nf_logs`. For each file help the user route it: + - **`results`**: a real tool output users want (report, summary, data file) + - **`logs`**: stdout/stderr from the tool + - **`.outputs-ignore`**: staging artifact, intermediate, version-info side effect, or DB file + `.outputs-ignore` lives at `modules/{name}/tests/.outputs-ignore` (one glob per line; `#` + comments and blanks allowed; `staging/**` is ignored by default). NOTE: this check only runs + when the tool **succeeds**, so it is masked on a profile that `tool_error`'d -- use + `undeclared_outputs_union` to see the full set. +- **`tool_error`** -- the tool crashed at runtime. Read **`error_class`**: + - `env_dependency` -- conda/singularity re-solved a too-new interpreter/dependency + (e.g. py>=3.12 `pkg_resources`, numpy2 `newshape`, biopython `SeqFeature.strand`, R + `readr`/`lifecycle` `deprecate_stop`). **Fix the env/recipe, NOT the test.** + - `tool_crash` / `staging_bug` / `fs_permission` / `unknown` -- fix the module/upstream or + the workspace; when `unknown`, read the `Command error:` block. + `reason` carries the real tool error (from `Command error:`), not the downstream nf-test + `NullPointerException`. + +`generate` gates interpretation (shown in Run Parameters and the `# generate=` header +of `summary.tsv`): +- **`generate=true`**: the `.snap` was regenerated under docker first, so docker passing is the + re-baseline; any drift shown is genuine (docker vs profile). `snapshot_stale` cannot occur. +- **`generate=false`**: docker **also** failing => `snapshot_stale` (run `--generate`). docker + passing while a profile drifts => genuine content drift. + +## Multi-profile layout & `summary.json` + +Structured results live at `logs/run-tests/{ts}/summary.json` (plus `summary.tsv`, whose first +line is `# generate=`). Prefer `summary.json` for machine-readable detail; the CLI text is +the human summary. Key fields: + +- `profiles[]`, `reference_profile` (`"docker"`). +- `results[].cells.{profile}`: `status`, `duration`, `reason`, `error_class` (tool_error only), + `undeclared_outputs[]`. +- `results[].undeclared_outputs_union`: undeclared files unioned across profiles (unmasks + profiles that `tool_error`'d). +- `results[].files[]`: per output file, the **cross-profile md5 matrix** -- `process`, `scope` + (`sample`/`run`; subworkflow multi-record), `field`, `name`, `md5:{profile -> hash|null}`, + `verdict`, `divergent_profiles[]`, plus: + - `verdict`: `stable` (equal across all profiles that ran) | `divergent` | `indeterminate` + (a profile didn't produce it) | `skip`. + - `comparable`: `false` = intrinsically non-hashable (gz / normalized -> byte md5 is + meaningless) => bucket **existence-only**; `verdict:"skip"`. + - `incomplete[]`: profiles that produced no file (e.g. a `tool_error`'d conda) => `verdict` + is `indeterminate`, NOT a false `stable`; re-check after fixing that profile. + - `kind:"versions"` + `tool_key`: a `versions.yml` -> bucket to `contains('')`. + This matrix is computed from actual runtime outputs, so it is populated **even on passing or + stale cells** -- an always-on divergence diagnostic (also useful for `add-*` at creation time). +- `results[].suggested_edit` (module/subworkflow only): the exact test change implied by the + verdicts -- `snapshot:[fields]` (stable), `existence:[fields]` (divergent content), + `contains:[{field,value}]` (divergent versions). Subworkflow fields are **scope-prefixed** + (`sample.`/`run.`, e.g. `sample.blast`, `run.versions`). Directly consumable and self-verifying + (diff against the committed test). Workflow tier is intentionally `.nftignore`-only, so it has no + `suggested_edit`; add the divergent globs to `workflows/**/tests/.nftignore` instead. + +## Diagnostic files (per profile) + +Layout: `logs/run-tests/{ts}/{tier}/{component}/{profile}/`: +- **`stdout.txt`** -- nf-test console, including the tool's own `Command error:` block. + Read this for **`tool_error` root cause**. +- **`stderr.txt`** -- nf-test assertions, including the `Different Snapshot` per-file md5 diff. + Read this for **drift / assertion detail**. +- **`outputs.txt`** -- `# Undeclared outputs:` list, or `# OK`. +- **`.nf-test/**`** -- preserved work tree (present for all cells, passing included), including + `meta/output_0.json` (record field -> output file paths) and `meta/nextflow.log`. + +Both `stdout.txt` and `stderr.txt` matter now, split by class (this replaces the old +"read stdout, not stderr" rule). ## Progressive Disclosure -The initial summary should be compact and scannable. When the user asks for deeper detail: - -- **Specific component**: Read its stdout file at - `logs/run-tests/{timestamp}/{tier}/{component}.stdout.txt` using the Read tool -- **Undeclared outputs**: Read the component's `.outputs.txt` file at - `logs/run-tests/{timestamp}/{tier}/{component}.outputs.txt` for the full file list. - Then read the module's `main.nf` to see the current `results` and `logs` - fields and advise where each undeclared file should go. -- **Abort errors**: Read the nextflow.log for the component - (focus on ERROR/WARN lines and last 50 lines). - To find the log path, re-run with `--json` and check the `nextflow_log` field, - or look in `logs/run-tests/{timestamp}/{tier}/{component}.stdout.txt` for the path. -- **Assertion details**: Read the stdout file and look for specific assertion - mismatch information - -Do NOT read nextflow.log or stdout files during the initial summary. +Keep the initial summary compact and scannable. Do NOT open `stdout`/`stderr`/`nextflow.log` +during the initial summary -- the status matrix, `reason`, `error_class`, and `files[]` usually +suffice. When the user asks for deeper detail: + +- **Specific component**: read its `summary.json` `results[]` entry first (cells, `reason`, + `error_class`, `files[]`, `suggested_edit`). Then, if needed, open + `{tier}/{component}/{profile}/stdout.txt` (tool_error) or that same dir's `stderr.txt` (drift diff). +- **Undeclared outputs**: use `undeclared_outputs_union` (or a cell's `undeclared_outputs[]`), + then read the module's `main.nf` output block to advise `results` / `logs` / `.outputs-ignore`. +- **Tool / abort errors**: read the `Command error:` block in `{profile}/stdout.txt`; the full + Nextflow log is at `{tier}/{component}/{profile}/.nf-test/tests/*/meta/nextflow.log` + (focus on ERROR/WARN and the last ~50 lines). +- **Drift bucketing**: use `files[]` + `suggested_edit`; cross-check with the + `Different Snapshot` block in `{profile}/stderr.txt`. ## Important Reminders -- CRITICAL: NEVER suggest "rerun with --update-snapshots" for non_reproducible - failures -- that does NOT fix the root cause -- When `params.generate` is true, NEVER suggest snapshot regeneration for - assertion failures -- snapshots were already regenerated during this run. - These represent non-deterministic output or incorrect test assertions. -- Always read `.stdout.txt` files for diagnostics, NOT `.stderr.txt` -- The `logs/run-tests/{timestamp}/` directory contains tier subdirectories based on what - was tested -- not all tiers are present in every run -- The `.nf-test/` work directories under component test dirs only exist for - failed tests (including `undeclared_outputs` failures -- preserved for review) -- If the user asks about a specific component, offer to read its stdout file - in full and check for nextflow.log +- CRITICAL: NEVER suggest `--update-snapshots` / snapshot regeneration for the drift statuses + (`output_drift`/`version_drift`/`version+output_drift`) or env-drift `tool_error`s. Regen does NOT fix profile divergence -- + migrate the test (sccmec pattern) or fix the env. `--generate` is the fix **only** for + `snapshot_stale`. +- `error_class: env_dependency` => fix the conda/singularity env or bioconda recipe, NOT the test. +- Read `{profile}/stdout.txt` for `tool_error` root cause and `{profile}/stderr.txt` for + drift/assertion diffs -- both matter. +- `undeclared_outputs` can be masked on a `tool_error`'d profile -- always check + `undeclared_outputs_union`. +- `files[]` verdicts: `comparable:false` (gz/normalized) -> existence-only; `verdict:indeterminate` + + `incomplete:[...]` -> a profile didn't run, re-check after fixing (never a clean bill). +- Not all tiers/profiles appear in every run; a component with no Galaxy image has + `galaxy:false` and no `singularity_galaxy` cell. +- `.nf-test/` work dirs are preserved per profile for **all** cells (passing included), so you can + inspect any profile's `meta/output_0.json` or work tree -- not just failures. ## Updating Baselines -Baselines file: `conf/test-times.json` +Baselines file: `conf/test-times.json`. Durations are **docker-based** (the CLI reports +"Docker duration"). To update baselines after a clean all-pass run, add `--update-baselines`: ``` @@ -95,30 +177,28 @@ bash .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia ``` This writes actual runtimes from the current run into the baselines file and updates the `_meta.updated` timestamp. Only entries for tested components are updated; other tiers -are left unchanged. - -After updating, re-run without `--update-baselines` to confirm anomalies are resolved. +are left unchanged. After updating, re-run without `--update-baselines` to confirm anomalies +are resolved. ## Interpreting Timing Anomalies -- **generate=true vs generate=false**: A `generate=true` run executes tests twice - (generate snapshots, then test against them). If baselines were recorded from a - `generate=true` run but the current run uses `generate=false`, tests will run at - ~0.5x baseline. This is expected, not suspicious. -- **Slow tests**: May reflect newly added test cases rather than regressions. Check - recent commits to the component's test file before flagging as a problem. -- **Only flag anomalies as concerning** when the `generate` parameter matches between - the baseline run and the current run. +Timing is measured against the **docker** profile. +- **generate=true vs generate=false**: a `generate=true` run executes tests twice (generate + snapshots, then test against them). If baselines were recorded from a `generate=true` run but + the current run uses `generate=false`, tests run at ~0.5x baseline -- expected, not suspicious. +- **Slow tests**: may reflect newly added test cases rather than regressions. Check recent + commits to the component's test file before flagging. +- **Only flag anomalies as concerning** when the `generate` parameter matches between the + baseline run and the current run. ## Self-Improvement -If you find yourself writing ad-hoc Python or bash to parse, explore, or extract data -from the CLI output, that logic should be added to this skill or the underlying -`bactopia-review-tests` CLI tool instead. Update the skill so future sessions don't -need to reinvent it. +If you find yourself writing ad-hoc Python or bash to parse, explore, or extract data from the +CLI output or `summary.json`, that logic should be added to this skill or the underlying +`bactopia-review-tests` CLI instead. Update the skill so future sessions don't reinvent it. -## JSON Output (Fallback) +## JSON Output -The `--json` flag is available as a fallback for programmatic access or when the -text output is too large. Use it with `--pretty` for readable JSON. See -`bactopia-review-tests --help` for details on JSON fields. +`logs/run-tests/{ts}/summary.json` is the primary structured source (schema above). The CLI can +also emit it with `--json` (add `--pretty` for readable output). See +`bactopia-review-tests --help` for details. diff --git a/conf/params.config b/conf/params.config index 8f48dbefe..e7be6c099 100644 --- a/conf/params.config +++ b/conf/params.config @@ -27,9 +27,9 @@ params { cleanup_workdir = false // Nextflow Profile Parameters - condadir = "${params.bactopia_cache}/conda" + condadir = System.getenv("NXF_CONDA_CACHEDIR") ?: "${params.bactopia_cache}/conda" singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false + singularity_pull_docker_container = System.getenv("NFT_SINGULARITY_PULL_DOCKER") == "true" force_rebuild = false container_opts = "" registry = "quay.io" diff --git a/conf/test.config b/conf/test.config index 4484ad00b..7e878d665 100644 --- a/conf/test.config +++ b/conf/test.config @@ -17,9 +17,8 @@ params { is_ci = true max_retry = 1 - condadir = System.getenv("BACTOPIA_CONDA") - singularity_pull_docker_container = true - test_data_dir = System.getenv("BACTOPIA_TESTS") + singularity_pull_docker_container = System.getenv("NFT_SINGULARITY_PULL_DOCKER") == "true" + test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" bactopia = params.bactopia_test ? "${params.test_data_dir}/${params.bactopia_test}" : null // General inputs diff --git a/conf/test_base.config b/conf/test_base.config index a140c4e31..88083f3db 100644 --- a/conf/test_base.config +++ b/conf/test_base.config @@ -2,7 +2,7 @@ params { bactopia_version = '4.1.0' bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ?: "${System.getenv('HOME')}/.bactopia" - condadir = "${params.bactopia_cache}/conda" + condadir = System.getenv("NXF_CONDA_CACHEDIR") ?: "${params.bactopia_cache}/conda" merge_folder = "merged-results" test_data_dir = System.getenv("BACTOPIA_TESTS") ?: "" is_ci = true @@ -15,8 +15,8 @@ params { // Nextflow Profile Parameters registry = "quay.io" - singularity_cache = "${params.bactopia_cache}/singularity" - singularity_pull_docker_container = false + singularity_cache = System.getenv("NXF_SINGULARITY_CACHEDIR") ?: "${params.bactopia_cache}/singularity" + singularity_pull_docker_container = System.getenv("NFT_SINGULARITY_PULL_DOCKER") == "true" container_opts = "" } diff --git a/modules/bactopia/assembler/tests/main.nf.test b/modules/bactopia/assembler/tests/main.nf.test index 14278169d..94c089b98 100644 --- a/modules/bactopia/assembler/tests/main.nf.test +++ b/modules/bactopia/assembler/tests/main.nf.test @@ -33,10 +33,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -68,10 +70,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -103,10 +107,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -139,10 +145,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -174,10 +182,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -212,10 +222,12 @@ nextflow_process { { assert process.success }, { assert record.fna == null }, { assert record.tsv == null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -248,10 +260,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } @@ -284,10 +298,12 @@ nextflow_process { { assert process.success }, { assert record.fna != null }, { assert record.tsv != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('assembly-scan') } ) } } diff --git a/modules/bactopia/qc/tests/main.nf.test b/modules/bactopia/qc/tests/main.nf.test index 7a9be3b1e..67dfdab03 100644 --- a/modules/bactopia/qc/tests/main.nf.test +++ b/modules/bactopia/qc/tests/main.nf.test @@ -35,10 +35,12 @@ nextflow_process { { assert process.success }, { assert record.r1 != null }, { assert record.r2 != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('fastp') } ) } } @@ -71,10 +73,12 @@ nextflow_process { assertAll( { assert process.success }, { assert record.se != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('fastp') } ) } } @@ -107,10 +111,12 @@ nextflow_process { assertAll( { assert process.success }, { assert record.lr != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('fastp') } ) } } @@ -147,10 +153,12 @@ nextflow_process { { assert record.r1 != null }, { assert record.r2 != null }, { assert record.lr != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('fastp') } ) } } @@ -185,10 +193,12 @@ nextflow_process { { assert process.success }, { assert record.r1 != null }, { assert record.r2 != null }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('fastp') } ) } } diff --git a/modules/bracken/tests/main.nf.test b/modules/bracken/tests/main.nf.test index adc458b2f..a2b9b2410 100644 --- a/modules/bracken/tests/main.nf.test +++ b/modules/bracken/tests/main.nf.test @@ -30,14 +30,18 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, record.tsv, record.kraken2_report, - record.bracken_report, - record.abundances, - record.versions - ).match() } + record.bracken_report + ).match() }, + // Non-reproducible outputs + { assert [ + record.abundances + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('bracken') } ) } } @@ -67,14 +71,18 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, record.tsv, record.kraken2_report, - record.bracken_report, - record.abundances, - record.versions - ).match() } + record.bracken_report + ).match() }, + // Non-reproducible outputs + { assert [ + record.abundances + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('bracken') } ) } } diff --git a/modules/eggnog/mapper/tests/main.nf.test b/modules/eggnog/mapper/tests/main.nf.test index 43470b746..83e9c3b50 100644 --- a/modules/eggnog/mapper/tests/main.nf.test +++ b/modules/eggnog/mapper/tests/main.nf.test @@ -28,10 +28,12 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('eggnog-mapper') } ) } } @@ -58,10 +60,12 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( - record.meta, - record.versions - ).match() } + record.meta + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('eggnog-mapper') } ) } } diff --git a/modules/gubbins/tests/main.nf.test b/modules/gubbins/tests/main.nf.test index ec6e11afe..f7db66261 100644 --- a/modules/gubbins/tests/main.nf.test +++ b/modules/gubbins/tests/main.nf.test @@ -26,11 +26,13 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.masked_aln, - record.versions - ).match() } + record.masked_aln + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('gubbins') } ) } } @@ -56,11 +58,13 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.masked_aln, - record.versions - ).match() } + record.masked_aln + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('gubbins') } ) } } diff --git a/modules/pasty/tests/main.nf.test b/modules/pasty/tests/main.nf.test index 19a7ffd7d..145ea937e 100644 --- a/modules/pasty/tests/main.nf.test +++ b/modules/pasty/tests/main.nf.test @@ -26,13 +26,17 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, + record.blast + ).match() }, + // Non-reproducible outputs + { assert [ record.tsv, - record.blast, - record.details, - record.versions - ).match() } + record.details + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('pasty') } ) } } diff --git a/modules/pasty/tests/main.nf.test.snap b/modules/pasty/tests/main.nf.test.snap index 3cdce4b7c..8e2887b85 100644 --- a/modules/pasty/tests/main.nf.test.snap +++ b/modules/pasty/tests/main.nf.test.snap @@ -9,14 +9,9 @@ "process_name": "pasty", "scope": "sample" }, - "GCF_000006765.tsv:md5,fdffd76c66ee57072cd5e8da474bba34", - "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258", - "GCF_000006765.details.tsv:md5,1215b1d8dd346836e07404c0a13c79f1", - [ - "versions.yml:md5,275841ecfb594907dd941a31a5e5f171" - ] + "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258" ], - "timestamp": "2026-07-29T01:28:30.918704318", + "timestamp": "2026-07-29T23:14:45.169553619", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pbptyper/tests/main.nf.test b/modules/pbptyper/tests/main.nf.test index a7e72fe19..1c95d33c7 100644 --- a/modules/pbptyper/tests/main.nf.test +++ b/modules/pbptyper/tests/main.nf.test @@ -26,12 +26,16 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, - record.blast, - record.versions - ).match() } + record.blast + ).match() }, + // Non-reproducible outputs + { assert [ + record.tsv + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('pbptyper') } ) } } diff --git a/modules/pbptyper/tests/main.nf.test.snap b/modules/pbptyper/tests/main.nf.test.snap index 658bb3bb8..4c1b34378 100644 --- a/modules/pbptyper/tests/main.nf.test.snap +++ b/modules/pbptyper/tests/main.nf.test.snap @@ -9,13 +9,9 @@ "process_name": "pbptyper", "scope": "sample" }, - "GCF_001457635.tsv:md5,1a21879bdaf7aac85a1f4e0fb0e59989", - "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967", - [ - "versions.yml:md5,be74af83bdcf74f71056df98990fdeda" - ] + "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967" ], - "timestamp": "2026-07-29T01:29:10.577383619", + "timestamp": "2026-07-29T21:59:05.002681726", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/quast/tests/main.nf.test b/modules/quast/tests/main.nf.test index 767a9673e..3fcb71eb2 100644 --- a/modules/quast/tests/main.nf.test +++ b/modules/quast/tests/main.nf.test @@ -27,11 +27,13 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, - record.versions - ).match() } + record.tsv + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('quast') } ) } } @@ -58,11 +60,13 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, - record.versions - ).match() } + record.tsv + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('quast') } ) } } @@ -89,11 +93,13 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, - record.versions - ).match() } + record.tsv + ).match() }, + // Non-reproducible outputs + { assert path(record.versions[0]).text.contains('quast') } ) } } diff --git a/modules/sccmec/tests/main.nf.test b/modules/sccmec/tests/main.nf.test index 6a7c43bdc..171c1f9d7 100644 --- a/modules/sccmec/tests/main.nf.test +++ b/modules/sccmec/tests/main.nf.test @@ -26,15 +26,19 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, record.targets, + record.regions + ).match() }, + // Non-reproducible outputs + { assert [ + record.tsv, record.target_details, - record.regions, - record.regions_details, - record.versions - ).match() } + record.regions_details + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('sccmec') } ) } } @@ -60,15 +64,19 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.tsv, record.targets, + record.regions + ).match() }, + // Non-reproducible outputs + { assert [ + record.tsv, record.target_details, - record.regions, - record.regions_details, - record.versions - ).match() } + record.regions_details + ].every { path(it).exists() } }, + { assert path(record.versions[0]).text.contains('sccmec') } ) } } diff --git a/modules/sccmec/tests/main.nf.test.snap b/modules/sccmec/tests/main.nf.test.snap index 4695bc6e6..5653a541e 100644 --- a/modules/sccmec/tests/main.nf.test.snap +++ b/modules/sccmec/tests/main.nf.test.snap @@ -9,16 +9,10 @@ "process_name": "sccmec", "scope": "sample" }, - "GCF_000017085.tsv:md5,da49131b3619e12fac7c1efef5e109d0", "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", - "GCF_000017085.targets.details.tsv:md5,8938065005a5f984229c09cd4d9f91e2", - "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6", - "GCF_000017085.regions.details.tsv:md5,d8568654b8455ddebf37283918805b46", - [ - "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" - ] + "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-29T01:29:16.80545439", + "timestamp": "2026-07-29T21:36:46.280663291", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -34,16 +28,10 @@ "process_name": "sccmec", "scope": "sample" }, - "GCF_000017085.tsv:md5,da49131b3619e12fac7c1efef5e109d0", "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", - "GCF_000017085.targets.details.tsv:md5,8938065005a5f984229c09cd4d9f91e2", - "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6", - "GCF_000017085.regions.details.tsv:md5,d8568654b8455ddebf37283918805b46", - [ - "versions.yml:md5,be2d2b5a56d601fba136df419d536c4a" - ] + "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-29T01:29:37.633384608", + "timestamp": "2026-07-29T21:36:55.946499331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sistr/tests/main.nf.test.snap b/modules/sistr/tests/main.nf.test.snap index 0ca559fb6..1159d7786 100644 --- a/modules/sistr/tests/main.nf.test.snap +++ b/modules/sistr/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-29T01:30:01.819167841", + "timestamp": "2026-07-29T21:42:14.544418614", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-29T01:30:43.557274508", + "timestamp": "2026-07-29T21:42:33.228698437", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/eggnog/tests/main.nf.test b/subworkflows/eggnog/tests/main.nf.test index dc42fac9c..b4e1834ea 100644 --- a/subworkflows/eggnog/tests/main.nf.test +++ b/subworkflows/eggnog/tests/main.nf.test @@ -30,10 +30,12 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert workflow.out.sample_outputs != null }, + // Reproducible outputs { assert snapshot( - sample.meta, - sample.versions + sample.meta ).match() }, + // Non-reproducible outputs + { assert path(sample.versions[0]).text.contains('eggnog-mapper') }, { assert sample.hits != null }, { assert sample.seed_orthologs != null }, { assert sample.annotations != null }, diff --git a/subworkflows/gubbins/tests/main.nf.test b/subworkflows/gubbins/tests/main.nf.test index 7c7a1b3f6..7e9be1c4c 100644 --- a/subworkflows/gubbins/tests/main.nf.test +++ b/subworkflows/gubbins/tests/main.nf.test @@ -29,14 +29,16 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( gubbins.meta, gubbins.masked_aln, - gubbins.versions, snpdists.meta, snpdists.tsv, snpdists.versions ).match() }, + // Non-reproducible outputs + { assert path(gubbins.versions[0]).text.contains('gubbins') }, { assert gubbins.results != null }, { assert snpdists.results != null } ) diff --git a/subworkflows/pasty/tests/main.nf.test b/subworkflows/pasty/tests/main.nf.test index ea932ec9e..d557e98ee 100644 --- a/subworkflows/pasty/tests/main.nf.test +++ b/subworkflows/pasty/tests/main.nf.test @@ -29,15 +29,19 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( sample.meta, - sample.tsv, sample.blast, - sample.details, - sample.versions, run.meta, run.versions ).match() }, + // Non-reproducible outputs + { assert [ + sample.tsv, + sample.details + ].every { path(it).exists() } }, + { assert path(sample.versions[0]).text.contains('pasty') }, { assert sample.results != null }, { assert run.csv != null }, { assert run.results != null } diff --git a/subworkflows/pasty/tests/main.nf.test.snap b/subworkflows/pasty/tests/main.nf.test.snap index c9ce75abc..a28502840 100644 --- a/subworkflows/pasty/tests/main.nf.test.snap +++ b/subworkflows/pasty/tests/main.nf.test.snap @@ -9,12 +9,7 @@ "process_name": "pasty", "scope": "sample" }, - "GCF_000006765.tsv:md5,fdffd76c66ee57072cd5e8da474bba34", "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258", - "GCF_000006765.details.tsv:md5,1215b1d8dd346836e07404c0a13c79f1", - [ - "versions.yml:md5,0356132ceb204ae511870a5e1fcb6d17" - ], { "id": "pasty-PASTY:CSVTK_CONCAT", "logs_dir": "merged-results/logs/pasty-concat/", @@ -27,7 +22,7 @@ "versions.yml:md5,d806f451289eb221f11075799712603e" ] ], - "timestamp": "2026-07-29T01:32:36.783413869", + "timestamp": "2026-07-29T21:47:10.992709384", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pbptyper/tests/main.nf.test b/subworkflows/pbptyper/tests/main.nf.test index a40e6f86a..61edf746a 100644 --- a/subworkflows/pbptyper/tests/main.nf.test +++ b/subworkflows/pbptyper/tests/main.nf.test @@ -29,14 +29,18 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( sample.meta, - sample.tsv, sample.blast, - sample.versions, run.meta, run.versions ).match() }, + // Non-reproducible outputs + { assert [ + sample.tsv + ].every { path(it).exists() } }, + { assert path(sample.versions[0]).text.contains('pbptyper') }, { assert sample.results != null }, { assert run.csv != null }, { assert run.results != null } diff --git a/subworkflows/pbptyper/tests/main.nf.test.snap b/subworkflows/pbptyper/tests/main.nf.test.snap index 722e3ac8e..2b55de6d5 100644 --- a/subworkflows/pbptyper/tests/main.nf.test.snap +++ b/subworkflows/pbptyper/tests/main.nf.test.snap @@ -9,11 +9,7 @@ "process_name": "pbptyper", "scope": "sample" }, - "GCF_001457635.tsv:md5,1a21879bdaf7aac85a1f4e0fb0e59989", "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967", - [ - "versions.yml:md5,47bb164e7435b20fe6e3e392e1bf06db" - ], { "id": "pbptyper-PBPTYPER:CSVTK_CONCAT", "logs_dir": "merged-results/logs/pbptyper-concat/", @@ -26,7 +22,7 @@ "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18" ] ], - "timestamp": "2026-07-29T01:33:07.555864876", + "timestamp": "2026-07-29T21:59:07.128112627", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/quast/tests/main.nf.test b/subworkflows/quast/tests/main.nf.test index 656e69b93..29934cab5 100644 --- a/subworkflows/quast/tests/main.nf.test +++ b/subworkflows/quast/tests/main.nf.test @@ -30,13 +30,15 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( sample.meta, sample.tsv, - sample.versions, run.meta, run.versions ).match() }, + // Non-reproducible outputs + { assert path(sample.versions[0]).text.contains('quast') }, { assert sample.results != null }, { assert run.csv != null }, { assert run.results != null } diff --git a/subworkflows/sccmec/tests/main.nf.test b/subworkflows/sccmec/tests/main.nf.test index 7ecaf7869..483cfc21d 100644 --- a/subworkflows/sccmec/tests/main.nf.test +++ b/subworkflows/sccmec/tests/main.nf.test @@ -29,17 +29,21 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( sample.meta, - sample.tsv, sample.targets, - sample.target_details, sample.regions, - sample.regions_details, - sample.versions, run.meta, run.versions ).match() }, + // Non-reproducible outputs + { assert [ + sample.tsv, + sample.target_details, + sample.regions_details + ].every { path(it).exists() } }, + { assert path(sample.versions[0]).text.contains('sccmec') }, { assert sample.results != null }, { assert run.csv != null }, { assert run.results != null } diff --git a/subworkflows/sccmec/tests/main.nf.test.snap b/subworkflows/sccmec/tests/main.nf.test.snap index e302037c1..05b727022 100644 --- a/subworkflows/sccmec/tests/main.nf.test.snap +++ b/subworkflows/sccmec/tests/main.nf.test.snap @@ -9,14 +9,8 @@ "process_name": "sccmec", "scope": "sample" }, - "GCF_000017085.tsv:md5,da49131b3619e12fac7c1efef5e109d0", "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", - "GCF_000017085.targets.details.tsv:md5,8938065005a5f984229c09cd4d9f91e2", "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6", - "GCF_000017085.regions.details.tsv:md5,d8568654b8455ddebf37283918805b46", - [ - "versions.yml:md5,cd9ded724580f921a03643bfaece66ee" - ], { "id": "sccmec-SCCMEC:CSVTK_CONCAT", "logs_dir": "merged-results/logs/sccmec-concat/", @@ -29,7 +23,7 @@ "versions.yml:md5,c6ede7b0533855a33c127cafa29de747" ] ], - "timestamp": "2026-07-29T01:33:09.452613063", + "timestamp": "2026-07-29T21:36:47.21301389", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sistr/tests/main.nf.test.snap b/subworkflows/sistr/tests/main.nf.test.snap index 5eb77cdce..8aeab78a7 100644 --- a/subworkflows/sistr/tests/main.nf.test.snap +++ b/subworkflows/sistr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-29T01:33:49.461261903", + "timestamp": "2026-07-29T21:42:15.395460849", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/teton/tests/main.nf.test b/subworkflows/teton/tests/main.nf.test index f6be5db92..58465aa45 100644 --- a/subworkflows/teton/tests/main.nf.test +++ b/subworkflows/teton/tests/main.nf.test @@ -41,12 +41,14 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( scrubber.meta, scrubber.versions, - bracken.meta, - bracken.versions + bracken.meta ).match() }, + // Non-reproducible outputs + { assert path(bracken.versions[0]).text.contains('bracken') }, { assert scrubber.results != null }, { assert bracken.results != null } ) diff --git a/tests/.nftignore b/tests/.nftignore index c83e71878..feb766962 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -2,4 +2,4 @@ **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} -**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,zip} +**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,yml,zip} diff --git a/workflows/bactopia-tools/bracken/tests/.nftignore b/workflows/bactopia-tools/bracken/tests/.nftignore index 72a5fcb38..e5b4181b4 100644 --- a/workflows/bactopia-tools/bracken/tests/.nftignore +++ b/workflows/bactopia-tools/bracken/tests/.nftignore @@ -1,3 +1,7 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.abundances.txt +**/bracken-adjusted.tsv +**/*.yml diff --git a/workflows/bactopia-tools/eggnog/tests/.nftignore b/workflows/bactopia-tools/eggnog/tests/.nftignore index 605485627..940a46def 100644 --- a/workflows/bactopia-tools/eggnog/tests/.nftignore +++ b/workflows/bactopia-tools/eggnog/tests/.nftignore @@ -3,3 +3,4 @@ bactopia-runs/**/nf-reports/*.{dot,html} **/*.emapper.* +**/*.yml diff --git a/workflows/bactopia-tools/pasty/tests/.nftignore b/workflows/bactopia-tools/pasty/tests/.nftignore index 72a5fcb38..8ee23c491 100644 --- a/workflows/bactopia-tools/pasty/tests/.nftignore +++ b/workflows/bactopia-tools/pasty/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.{tsv,yml} diff --git a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap index 63283d5f0..07f83b486 100644 --- a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap @@ -38,15 +38,10 @@ "bactopia-runs/pasty/nf-reports/pasty-timeline.html" ], [ - "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258", - "GCF_000006765.details.tsv:md5,1215b1d8dd346836e07404c0a13c79f1", - "GCF_000006765.tsv:md5,fdffd76c66ee57072cd5e8da474bba34", - "versions.yml:md5,0356132ceb204ae511870a5e1fcb6d17", - "versions.yml:md5,d806f451289eb221f11075799712603e", - "pasty.tsv:md5,3f0b647b733d1c01212c1f475527aef4" + ] ], - "timestamp": "2026-07-29T01:37:15.05939135", + "timestamp": "2026-07-29T21:47:17.211995656", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pbptyper/tests/.nftignore b/workflows/bactopia-tools/pbptyper/tests/.nftignore index 72a5fcb38..8ee23c491 100644 --- a/workflows/bactopia-tools/pbptyper/tests/.nftignore +++ b/workflows/bactopia-tools/pbptyper/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.{tsv,yml} diff --git a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap index 668966885..ad190aa3a 100644 --- a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap @@ -37,14 +37,10 @@ "bactopia-runs/pbptyper/nf-reports/pbptyper-timeline.html" ], [ - "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967", - "GCF_001457635.tsv:md5,1a21879bdaf7aac85a1f4e0fb0e59989", - "versions.yml:md5,47bb164e7435b20fe6e3e392e1bf06db", - "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18", - "pbptyper.tsv:md5,34edc1f9346b74b74ef4446d270e6d57" + ] ], - "timestamp": "2026-07-29T01:37:53.634175779", + "timestamp": "2026-07-29T21:59:12.623312651", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/quast/tests/.nftignore b/workflows/bactopia-tools/quast/tests/.nftignore index 72a5fcb38..f1d2aaa1d 100644 --- a/workflows/bactopia-tools/quast/tests/.nftignore +++ b/workflows/bactopia-tools/quast/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.yml diff --git a/workflows/bactopia-tools/sccmec/tests/.nftignore b/workflows/bactopia-tools/sccmec/tests/.nftignore index 72a5fcb38..8ee23c491 100644 --- a/workflows/bactopia-tools/sccmec/tests/.nftignore +++ b/workflows/bactopia-tools/sccmec/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.{tsv,yml} diff --git a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap index c3d91fa39..8cf4b46ce 100644 --- a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap @@ -40,17 +40,10 @@ "bactopia-runs/sccmec/nf-reports/sccmec-timeline.html" ], [ - "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6", - "GCF_000017085.regions.details.tsv:md5,d8568654b8455ddebf37283918805b46", - "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", - "GCF_000017085.targets.details.tsv:md5,8938065005a5f984229c09cd4d9f91e2", - "GCF_000017085.tsv:md5,da49131b3619e12fac7c1efef5e109d0", - "versions.yml:md5,cd9ded724580f921a03643bfaece66ee", - "versions.yml:md5,c6ede7b0533855a33c127cafa29de747", - "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" + ] ], - "timestamp": "2026-07-29T01:38:24.795826641", + "timestamp": "2026-07-29T21:37:10.373092259", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -97,17 +90,10 @@ "bactopia-runs/sccmec/nf-reports/sccmec-timeline.html" ], [ - "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6", - "GCF_000017085.regions.details.tsv:md5,d8568654b8455ddebf37283918805b46", - "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", - "GCF_000017085.targets.details.tsv:md5,8938065005a5f984229c09cd4d9f91e2", - "GCF_000017085.tsv:md5,da49131b3619e12fac7c1efef5e109d0", - "versions.yml:md5,cd9ded724580f921a03643bfaece66ee", - "versions.yml:md5,c6ede7b0533855a33c127cafa29de747", - "sccmec.tsv:md5,7b28813993e6b0b48532bb2b161bc975" + ] ], - "timestamp": "2026-07-29T01:37:42.751129903", + "timestamp": "2026-07-29T21:36:53.434687545", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigatyper/tests/.nftignore b/workflows/bactopia-tools/shigatyper/tests/.nftignore index 72a5fcb38..577bb935a 100644 --- a/workflows/bactopia-tools/shigatyper/tests/.nftignore +++ b/workflows/bactopia-tools/shigatyper/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/shigatyper.tsv diff --git a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap index af8750541..10008772e 100644 --- a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-29T01:38:21.809046788", + "timestamp": "2026-07-29T21:42:20.750099646", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/snippy/tests/.nftignore b/workflows/bactopia-tools/snippy/tests/.nftignore index c066d9856..df4cdff24 100644 --- a/workflows/bactopia-tools/snippy/tests/.nftignore +++ b/workflows/bactopia-tools/snippy/tests/.nftignore @@ -5,3 +5,4 @@ bactopia-runs/**/nf-reports/*.{dot,html} **/*.{bam,bai,bionj,contree,iqtree,mldist,nex,phylip,tre,treefile,txt,ufboot} **/*.per_branch_statistics.csv **/core-snp.masked.distance.tsv +**/*.yml diff --git a/workflows/bactopia-tools/staphtyper/tests/.nftignore b/workflows/bactopia-tools/staphtyper/tests/.nftignore index 72a5fcb38..8ee23c491 100644 --- a/workflows/bactopia-tools/staphtyper/tests/.nftignore +++ b/workflows/bactopia-tools/staphtyper/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/*.{tsv,yml} diff --git a/workflows/bactopia-tools/stecfinder/tests/.nftignore b/workflows/bactopia-tools/stecfinder/tests/.nftignore index 72a5fcb38..b207a4cd8 100644 --- a/workflows/bactopia-tools/stecfinder/tests/.nftignore +++ b/workflows/bactopia-tools/stecfinder/tests/.nftignore @@ -1,3 +1,5 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} + +**/stecfinder.tsv diff --git a/workflows/cleanyerreads/tests/.nftignore b/workflows/cleanyerreads/tests/.nftignore index c83e71878..feb766962 100644 --- a/workflows/cleanyerreads/tests/.nftignore +++ b/workflows/cleanyerreads/tests/.nftignore @@ -2,4 +2,4 @@ **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} -**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,zip} +**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,yml,zip} diff --git a/workflows/staphopia/tests/.nftignore b/workflows/staphopia/tests/.nftignore index 895a010d2..79090ef78 100644 --- a/workflows/staphopia/tests/.nftignore +++ b/workflows/staphopia/tests/.nftignore @@ -2,4 +2,4 @@ **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} -**/*.{corrections,hist,histogram,json,msh,sig,tab,txt,tsv,zip} +**/*.{corrections,hist,histogram,json,msh,sig,tab,txt,tsv,yml,zip} diff --git a/workflows/teton/tests/.nftignore b/workflows/teton/tests/.nftignore index c83e71878..feb766962 100644 --- a/workflows/teton/tests/.nftignore +++ b/workflows/teton/tests/.nftignore @@ -2,4 +2,4 @@ **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} -**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,zip} +**/*.{corrections,hist,histogram,json,msh,sig,txt,tsv,yml,zip} From 8259f98aa93dcb9b0a0bd027a969aa2b84fdf811 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Thu, 30 Jul 2026 10:46:52 -0600 Subject: [PATCH 32/43] update snap shots --- modules/abricate/run/tests/main.nf.test.snap | 2 +- .../abricate/summary/tests/main.nf.test.snap | 2 +- modules/abritamr/run/tests/main.nf.test.snap | 4 +- modules/agrvate/tests/main.nf.test.snap | 4 +- .../amrfinderplus/run/tests/main.nf.test.snap | 4 +- modules/ariba/run/tests/main.nf.test.snap | 2 +- .../assembler/tests/main.nf.test.snap | 56 +++------- .../bactopia/gather/tests/main.nf.test.snap | 16 +-- modules/bactopia/qc/tests/main.nf.test.snap | 35 ++---- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- .../bactopia/teton/tests/main.nf.test.snap | 4 +- modules/bakta/run/tests/main.nf.test.snap | 4 +- modules/blast/blastn/tests/main.nf.test.snap | 2 +- modules/blast/blastp/tests/main.nf.test.snap | 2 +- modules/blast/blastx/tests/main.nf.test.snap | 2 +- modules/blast/tblastn/tests/main.nf.test.snap | 2 +- modules/blast/tblastx/tests/main.nf.test.snap | 2 +- modules/bracken/tests/main.nf.test.snap | 16 +-- modules/btyper3/tests/main.nf.test.snap | 4 +- modules/busco/tests/main.nf.test.snap | 4 +- .../checkm/lineagewf/tests/main.nf.test.snap | 4 +- .../checkm2/predict/tests/main.nf.test.snap | 4 +- modules/clermontyping/tests/main.nf.test.snap | 4 +- modules/clonalframeml/tests/main.nf.test.snap | 4 +- modules/csvtk/concat/tests/main.nf.test.snap | 4 +- modules/csvtk/join/tests/main.nf.test.snap | 4 +- modules/deacon/filter/tests/main.nf.test.snap | 6 +- .../defensefinder/run/tests/main.nf.test.snap | 2 +- modules/ectyper/tests/main.nf.test.snap | 4 +- modules/eggnog/mapper/tests/main.nf.test.snap | 14 +-- modules/emmtyper/tests/main.nf.test.snap | 6 +- modules/fastani/tests/main.nf.test.snap | 4 +- modules/gamma/tests/main.nf.test.snap | 4 +- modules/genomedl/tests/main.nf.test.snap | 6 +- .../genotyphi/parse/tests/main.nf.test.snap | 2 +- modules/gigatyper/tests/main.nf.test.snap | 2 +- .../gtdbtk/classifywf/tests/main.nf.test.snap | 2 +- modules/gubbins/tests/main.nf.test.snap | 14 +-- modules/hicap/tests/main.nf.test.snap | 8 +- modules/hpsuissero/tests/main.nf.test.snap | 4 +- modules/iqtree/tests/main.nf.test.snap | 4 +- modules/ismapper/tests/main.nf.test.snap | 2 +- modules/kleborate/tests/main.nf.test.snap | 2 +- modules/kraken2/tests/main.nf.test.snap | 4 +- modules/legsta/tests/main.nf.test.snap | 2 +- modules/lissero/tests/main.nf.test.snap | 4 +- modules/mash/dist/tests/main.nf.test.snap | 4 +- modules/mashtree/tests/main.nf.test.snap | 2 +- modules/mcroni/tests/main.nf.test.snap | 4 +- modules/meningotype/tests/main.nf.test.snap | 4 +- modules/merlin/dist/tests/main.nf.test.snap | 4 +- modules/midas/species/tests/main.nf.test.snap | 4 +- modules/mlst/tests/main.nf.test.snap | 2 +- .../mobsuite/recon/tests/main.nf.test.snap | 6 +- .../mykrobe/predict/tests/main.nf.test.snap | 2 +- modules/ngmaster/tests/main.nf.test.snap | 4 +- modules/nohuman/run/tests/main.nf.test.snap | 6 +- modules/panaroo/run/tests/main.nf.test.snap | 2 +- modules/pasty/tests/main.nf.test.snap | 2 +- modules/pbptyper/tests/main.nf.test.snap | 2 +- modules/phispy/tests/main.nf.test.snap | 2 +- modules/pirate/tests/main.nf.test.snap | 2 +- modules/plasmidfinder/tests/main.nf.test.snap | 4 +- modules/pneumocat/tests/main.nf.test.snap | 2 +- modules/prokka/tests/main.nf.test.snap | 6 +- modules/quast/tests/main.nf.test.snap | 21 +--- modules/rgi/heatmap/tests/main.nf.test.snap | 2 +- modules/rgi/main/tests/main.nf.test.snap | 6 +- modules/roary/tests/main.nf.test.snap | 2 +- modules/sccmec/tests/main.nf.test.snap | 4 +- modules/scoary/tests/main.nf.test.snap | 2 +- modules/seqsero2/tests/main.nf.test.snap | 4 +- modules/seroba/run/tests/main.nf.test.snap | 2 +- modules/shigapass/tests/main.nf.test.snap | 4 +- modules/shigatyper/tests/main.nf.test.snap | 2 +- modules/shigeifinder/tests/main.nf.test.snap | 4 +- modules/sistr/tests/main.nf.test.snap | 4 +- modules/snippy/core/tests/main.nf.test.snap | 2 +- modules/snippy/run/tests/main.nf.test.snap | 4 +- modules/snpdists/tests/main.nf.test.snap | 2 +- modules/spatyper/tests/main.nf.test.snap | 4 +- .../scrub/tests/main.nf.test.snap | 4 +- modules/ssuissero/tests/main.nf.test.snap | 4 +- .../staphopiasccmec/tests/main.nf.test.snap | 4 +- modules/staphscan/tests/main.nf.test.snap | 2 +- modules/stecfinder/tests/main.nf.test.snap | 6 +- modules/stxtyper/tests/main.nf.test.snap | 2 +- modules/sylph/profile/tests/main.nf.test.snap | 4 +- .../collate/tests/main.nf.test.snap | 2 +- .../profile/tests/main.nf.test.snap | 6 +- modules/traitar/run/tests/main.nf.test.snap | 4 +- subworkflows/abricate/tests/main.nf.test.snap | 2 +- subworkflows/abritamr/tests/main.nf.test.snap | 2 +- subworkflows/agrvate/tests/main.nf.test.snap | 2 +- .../amrfinderplus/tests/main.nf.test.snap | 2 +- subworkflows/ariba/tests/main.nf.test.snap | 2 +- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- subworkflows/bakta/tests/main.nf.test.snap | 2 +- subworkflows/blastn/tests/main.nf.test.snap | 2 +- subworkflows/blastp/tests/main.nf.test.snap | 2 +- subworkflows/blastx/tests/main.nf.test.snap | 2 +- subworkflows/btyper3/tests/main.nf.test.snap | 2 +- subworkflows/busco/tests/main.nf.test.snap | 2 +- subworkflows/checkm/tests/main.nf.test.snap | 2 +- subworkflows/checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../clonalframeml/tests/main.nf.test.snap | 2 +- subworkflows/deacon/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- subworkflows/ectyper/tests/main.nf.test.snap | 2 +- subworkflows/eggnog/tests/main.nf.test.snap | 7 +- subworkflows/emmtyper/tests/main.nf.test.snap | 2 +- subworkflows/fastani/tests/main.nf.test.snap | 2 +- subworkflows/gamma/tests/main.nf.test.snap | 2 +- subworkflows/genomedl/tests/main.nf.test.snap | 6 +- .../genotyphi/tests/main.nf.test.snap | 2 +- .../gigatyper/tests/main.nf.test.snap | 2 +- subworkflows/gtdb/tests/main.nf.test.snap | 2 +- subworkflows/gubbins/tests/main.nf.test.snap | 5 +- subworkflows/hicap/tests/main.nf.test.snap | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- subworkflows/iqtree/tests/main.nf.test.snap | 2 +- subworkflows/ismapper/tests/main.nf.test.snap | 2 +- .../kleborate/tests/main.nf.test.snap | 2 +- subworkflows/kraken2/tests/main.nf.test.snap | 2 +- subworkflows/legsta/tests/main.nf.test.snap | 2 +- subworkflows/lissero/tests/main.nf.test.snap | 2 +- subworkflows/mashdist/tests/main.nf.test.snap | 2 +- subworkflows/mashtree/tests/main.nf.test.snap | 2 +- subworkflows/mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../merlindist/tests/main.nf.test.snap | 2 +- subworkflows/midas/tests/main.nf.test.snap | 2 +- subworkflows/mlst/tests/main.nf.test.snap | 2 +- subworkflows/mobsuite/tests/main.nf.test.snap | 2 +- subworkflows/mykrobe/tests/main.nf.test.snap | 2 +- subworkflows/ngmaster/tests/main.nf.test.snap | 2 +- subworkflows/nohuman/tests/main.nf.test.snap | 2 +- subworkflows/panaroo/tests/main.nf.test.snap | 2 +- .../pangenome/tests/main.nf.test.snap | 2 +- subworkflows/pasty/tests/main.nf.test.snap | 2 +- subworkflows/pbptyper/tests/main.nf.test.snap | 2 +- subworkflows/phispy/tests/main.nf.test.snap | 2 +- subworkflows/pirate/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../pneumocat/tests/main.nf.test.snap | 2 +- subworkflows/prokka/tests/main.nf.test.snap | 2 +- subworkflows/quast/tests/main.nf.test.snap | 5 +- subworkflows/rgi/tests/main.nf.test.snap | 2 +- subworkflows/roary/tests/main.nf.test.snap | 2 +- subworkflows/sccmec/tests/main.nf.test.snap | 2 +- subworkflows/scoary/tests/main.nf.test.snap | 2 +- subworkflows/scrubber/tests/main.nf.test.snap | 4 +- subworkflows/seqsero2/tests/main.nf.test.snap | 2 +- subworkflows/seroba/tests/main.nf.test.snap | 2 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- subworkflows/sistr/tests/main.nf.test.snap | 2 +- .../snippy/core/tests/main.nf.test.snap | 2 +- .../snippy/run/tests/main.nf.test.snap | 2 +- subworkflows/snpdists/tests/main.nf.test.snap | 2 +- subworkflows/spatyper/tests/main.nf.test.snap | 2 +- .../srahumanscrubber/tests/main.nf.test.snap | 2 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../staphopiasccmec/tests/main.nf.test.snap | 2 +- .../staphscan/tests/main.nf.test.snap | 2 +- .../stecfinder/tests/main.nf.test.snap | 2 +- subworkflows/stxtyper/tests/main.nf.test.snap | 2 +- subworkflows/sylph/tests/main.nf.test.snap | 2 +- subworkflows/tblastn/tests/main.nf.test.snap | 2 +- subworkflows/tblastx/tests/main.nf.test.snap | 2 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- subworkflows/teton/tests/main.nf.test.snap | 7 +- subworkflows/traitar/tests/main.nf.test.snap | 2 +- tests/main.nf.test.snap | 104 +++--------------- .../abricate/tests/main.nf.test.snap | 2 +- .../abritamr/tests/main.nf.test.snap | 2 +- .../agrvate/tests/main.nf.test.snap | 4 +- .../amrfinderplus/tests/main.nf.test.snap | 4 +- .../ariba/tests/main.nf.test.snap | 2 +- .../bakta/tests/main.nf.test.snap | 4 +- .../blastn/tests/main.nf.test.snap | 6 +- .../blastp/tests/main.nf.test.snap | 6 +- .../blastx/tests/main.nf.test.snap | 6 +- .../bracken/tests/main.nf.test.snap | 20 +--- .../btyper3/tests/main.nf.test.snap | 2 +- .../busco/tests/main.nf.test.snap | 2 +- .../checkm/tests/main.nf.test.snap | 2 +- .../checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- .../ectyper/tests/main.nf.test.snap | 2 +- .../eggnog/tests/main.nf.test.snap | 4 +- .../emmtyper/tests/main.nf.test.snap | 4 +- .../fastani/tests/main.nf.test.snap | 6 +- .../gamma/tests/main.nf.test.snap | 2 +- .../genotyphi/tests/main.nf.test.snap | 2 +- .../gigatyper/tests/main.nf.test.snap | 2 +- .../gtdb/tests/main.nf.test.snap | 2 +- .../hicap/tests/main.nf.test.snap | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- .../ismapper/tests/main.nf.test.snap | 2 +- .../kleborate/tests/main.nf.test.snap | 2 +- .../kraken2/tests/main.nf.test.snap | 4 +- .../legsta/tests/main.nf.test.snap | 2 +- .../lissero/tests/main.nf.test.snap | 2 +- .../mashdist/tests/main.nf.test.snap | 2 +- .../mashtree/tests/main.nf.test.snap | 4 +- .../mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../merlin/tests/main.nf.test.snap | 4 +- .../midas/tests/main.nf.test.snap | 4 +- .../mlst/tests/main.nf.test.snap | 2 +- .../mobsuite/tests/main.nf.test.snap | 2 +- .../mykrobe/tests/main.nf.test.snap | 2 +- .../ngmaster/tests/main.nf.test.snap | 2 +- .../pangenome/tests/main.nf.test.snap | 12 +- .../pasty/tests/main.nf.test.snap | 2 +- .../pbptyper/tests/main.nf.test.snap | 2 +- .../phispy/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../pneumocat/tests/main.nf.test.snap | 2 +- .../prokka/tests/main.nf.test.snap | 2 +- .../quast/tests/main.nf.test.snap | 4 +- .../rgi/tests/main.nf.test.snap | 2 +- .../sccmec/tests/main.nf.test.snap | 4 +- .../scrubber/tests/main.nf.test.snap | 6 +- .../seqsero2/tests/main.nf.test.snap | 2 +- .../seroba/tests/main.nf.test.snap | 2 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../shigatyper/tests/main.nf.test.snap | 5 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- .../sistr/tests/main.nf.test.snap | 2 +- .../snippy/tests/main.nf.test.snap | 85 ++------------ .../spatyper/tests/main.nf.test.snap | 4 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../staphscan/tests/main.nf.test.snap | 2 +- .../staphtyper/tests/main.nf.test.snap | 24 +--- .../stecfinder/tests/main.nf.test.snap | 5 +- .../stxtyper/tests/main.nf.test.snap | 2 +- .../sylph/tests/main.nf.test.snap | 2 +- .../tblastn/tests/main.nf.test.snap | 4 +- .../tblastx/tests/main.nf.test.snap | 6 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- .../traitar/tests/main.nf.test.snap | 2 +- .../cleanyerreads/tests/main.nf.test.snap | 14 +-- workflows/staphopia/tests/main.nf.test.snap | 22 +--- workflows/teton/tests/main.nf.test.snap | 48 +------- 249 files changed, 431 insertions(+), 736 deletions(-) diff --git a/modules/abricate/run/tests/main.nf.test.snap b/modules/abricate/run/tests/main.nf.test.snap index 866d21abd..c1743a3f3 100644 --- a/modules/abricate/run/tests/main.nf.test.snap +++ b/modules/abricate/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,7baef5ee36e4b70a7227723d89bf97ea" ] ], - "timestamp": "2026-07-29T01:28:24.214941395", + "timestamp": "2026-07-30T00:27:33.430771963", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abricate/summary/tests/main.nf.test.snap b/modules/abricate/summary/tests/main.nf.test.snap index 193599562..72defcfb4 100644 --- a/modules/abricate/summary/tests/main.nf.test.snap +++ b/modules/abricate/summary/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,87422ca0c784de85ba93ac7352052d82" ] ], - "timestamp": "2026-07-29T01:28:24.562552282", + "timestamp": "2026-07-30T00:27:37.80307685", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abritamr/run/tests/main.nf.test.snap b/modules/abritamr/run/tests/main.nf.test.snap index b2c0bf356..339654465 100644 --- a/modules/abritamr/run/tests/main.nf.test.snap +++ b/modules/abritamr/run/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-29T01:32:45.809785745", + "timestamp": "2026-07-30T00:31:50.164649198", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-29T01:37:03.995078677", + "timestamp": "2026-07-30T00:36:04.650621711", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/agrvate/tests/main.nf.test.snap b/modules/agrvate/tests/main.nf.test.snap index 8f434b286..49d07971c 100644 --- a/modules/agrvate/tests/main.nf.test.snap +++ b/modules/agrvate/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-29T01:28:45.557959581", + "timestamp": "2026-07-30T00:27:45.78711724", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-29T01:28:29.676580462", + "timestamp": "2026-07-30T00:27:30.771873199", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/amrfinderplus/run/tests/main.nf.test.snap b/modules/amrfinderplus/run/tests/main.nf.test.snap index 962af0f7e..1c8162544 100644 --- a/modules/amrfinderplus/run/tests/main.nf.test.snap +++ b/modules/amrfinderplus/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-29T01:28:44.847096965", + "timestamp": "2026-07-30T00:27:39.164054105", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-29T01:29:08.350914695", + "timestamp": "2026-07-30T00:28:02.254823537", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ariba/run/tests/main.nf.test.snap b/modules/ariba/run/tests/main.nf.test.snap index ab9fbd055..2cae6a94a 100644 --- a/modules/ariba/run/tests/main.nf.test.snap +++ b/modules/ariba/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2d20a87ab1578332cae79c947a52e8f8" ] ], - "timestamp": "2026-07-29T01:28:59.378421092", + "timestamp": "2026-07-30T00:28:25.295295632", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/assembler/tests/main.nf.test.snap b/modules/bactopia/assembler/tests/main.nf.test.snap index 61164b1ae..a82a0f283 100644 --- a/modules/bactopia/assembler/tests/main.nf.test.snap +++ b/modules/bactopia/assembler/tests/main.nf.test.snap @@ -12,12 +12,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:43:03.413255267", + "timestamp": "2026-07-30T00:43:04.309806358", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -36,12 +33,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:47:26.293537587", + "timestamp": "2026-07-30T00:49:46.54340004", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -60,12 +54,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:46:59.67652929", + "timestamp": "2026-07-30T00:49:02.152014818", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -84,12 +75,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:45:27.327994741", + "timestamp": "2026-07-30T00:46:56.905269041", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -108,12 +96,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:45:57.813478176", + "timestamp": "2026-07-30T00:47:41.368206613", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -132,12 +117,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:30:53.217753604", + "timestamp": "2026-07-30T00:29:57.965081441", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -156,12 +138,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:31:33.844573405", + "timestamp": "2026-07-30T00:30:36.673420092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -180,12 +159,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,278ebf6d69552124610809b2ea1520fa" - ] + } ], - "timestamp": "2026-07-29T01:35:24.570380526", + "timestamp": "2026-07-30T00:34:18.063960274", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/gather/tests/main.nf.test.snap b/modules/bactopia/gather/tests/main.nf.test.snap index f9bb23c5d..40798ef3a 100644 --- a/modules/bactopia/gather/tests/main.nf.test.snap +++ b/modules/bactopia/gather/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:29:33.799764907", + "timestamp": "2026-07-30T00:28:30.680970188", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:29:57.878211735", + "timestamp": "2026-07-30T00:28:54.243545308", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -70,7 +70,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:31:40.907151631", + "timestamp": "2026-07-30T00:30:31.639769887", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:31:19.73009397", + "timestamp": "2026-07-30T00:30:12.165437052", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -121,7 +121,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:30:34.967253801", + "timestamp": "2026-07-30T00:29:29.44934561", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:30:56.298486348", + "timestamp": "2026-07-30T00:29:51.043793603", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -173,7 +173,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:28:47.975892113", + "timestamp": "2026-07-30T00:27:44.840771684", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -199,7 +199,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-29T01:29:11.193972235", + "timestamp": "2026-07-30T00:28:07.005802392", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/qc/tests/main.nf.test.snap b/modules/bactopia/qc/tests/main.nf.test.snap index bbd592de9..93279d1ae 100644 --- a/modules/bactopia/qc/tests/main.nf.test.snap +++ b/modules/bactopia/qc/tests/main.nf.test.snap @@ -12,12 +12,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" - ] + } ], - "timestamp": "2026-07-29T01:29:53.240079953", + "timestamp": "2026-07-30T00:29:03.659398485", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -36,12 +33,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" - ] + } ], - "timestamp": "2026-07-29T01:30:53.187400287", + "timestamp": "2026-07-30T00:30:04.521158614", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -60,12 +54,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" - ] + } ], - "timestamp": "2026-07-29T01:33:36.18953171", + "timestamp": "2026-07-30T00:32:40.710016356", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -84,12 +75,9 @@ "scope": "sample", "single_end": true, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" - ] + } ], - "timestamp": "2026-07-29T01:31:45.972044885", + "timestamp": "2026-07-30T00:30:51.266979238", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -108,12 +96,9 @@ "scope": "sample", "single_end": false, "species": "Portiera aleyrodidarum" - }, - [ - "versions.yml:md5,039e8b06ff0140cc2616c36d90ded521" - ] + } ], - "timestamp": "2026-07-29T01:34:13.427660919", + "timestamp": "2026-07-30T00:33:22.799446708", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/sketcher/tests/main.nf.test.snap b/modules/bactopia/sketcher/tests/main.nf.test.snap index 19caaf410..f0aaa9de8 100644 --- a/modules/bactopia/sketcher/tests/main.nf.test.snap +++ b/modules/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,559fcd38f7410952b8da3f25f165d6fd" ] ], - "timestamp": "2026-07-29T01:31:45.215794434", + "timestamp": "2026-07-30T00:30:16.285079051", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/teton/tests/main.nf.test.snap b/modules/bactopia/teton/tests/main.nf.test.snap index b33c23d3b..8c307fde3 100644 --- a/modules/bactopia/teton/tests/main.nf.test.snap +++ b/modules/bactopia/teton/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-29T01:28:35.254165018", + "timestamp": "2026-07-30T00:27:42.124626112", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-29T01:28:51.543511604", + "timestamp": "2026-07-30T00:27:57.82836261", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bakta/run/tests/main.nf.test.snap b/modules/bakta/run/tests/main.nf.test.snap index 1b2575d9a..10d303bee 100644 --- a/modules/bakta/run/tests/main.nf.test.snap +++ b/modules/bakta/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-29T01:32:31.402053192", + "timestamp": "2026-07-30T00:31:33.386526961", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-29T01:35:20.61960942", + "timestamp": "2026-07-30T00:34:20.087738169", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastn/tests/main.nf.test.snap b/modules/blast/blastn/tests/main.nf.test.snap index 34cd85883..f7ebe288e 100644 --- a/modules/blast/blastn/tests/main.nf.test.snap +++ b/modules/blast/blastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,45d0dac48620078713131f03b02bd14a" ] ], - "timestamp": "2026-07-29T01:28:25.15166746", + "timestamp": "2026-07-30T00:27:30.248901271", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastp/tests/main.nf.test.snap b/modules/blast/blastp/tests/main.nf.test.snap index ce7546b71..dceaf21c1 100644 --- a/modules/blast/blastp/tests/main.nf.test.snap +++ b/modules/blast/blastp/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,617451a4191edeef7d2c7fb101c1ac14" ] ], - "timestamp": "2026-07-29T01:28:25.530081089", + "timestamp": "2026-07-30T00:27:30.370813436", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastx/tests/main.nf.test.snap b/modules/blast/blastx/tests/main.nf.test.snap index 3c7796fcd..1a37f6c1c 100644 --- a/modules/blast/blastx/tests/main.nf.test.snap +++ b/modules/blast/blastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6a3a4c2a4204ac747af921720f265d86" ] ], - "timestamp": "2026-07-29T01:28:29.086481152", + "timestamp": "2026-07-30T00:27:36.683267065", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastn/tests/main.nf.test.snap b/modules/blast/tblastn/tests/main.nf.test.snap index d96fa311a..111b7947e 100644 --- a/modules/blast/tblastn/tests/main.nf.test.snap +++ b/modules/blast/tblastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,24c7db9cd7b317dcf8ad2057a04b2860" ] ], - "timestamp": "2026-07-29T01:28:28.223585438", + "timestamp": "2026-07-30T00:27:30.442772949", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastx/tests/main.nf.test.snap b/modules/blast/tblastx/tests/main.nf.test.snap index 135ece600..0cc347d12 100644 --- a/modules/blast/tblastx/tests/main.nf.test.snap +++ b/modules/blast/tblastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2d402efb20baa10e7b3af88ef3f2312d" ] ], - "timestamp": "2026-07-29T01:28:23.804195768", + "timestamp": "2026-07-30T00:27:32.057380628", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bracken/tests/main.nf.test.snap b/modules/bracken/tests/main.nf.test.snap index 05f202cb3..9e228543a 100644 --- a/modules/bracken/tests/main.nf.test.snap +++ b/modules/bracken/tests/main.nf.test.snap @@ -13,13 +13,9 @@ }, "SRR2838702.bracken.tsv:md5,ea649edb882ed5adfb200f740bcdf17e", "SRR2838702.kraken2.report.txt:md5,29a9ad9bb9b9b17a43e969f82c6e3e9f", - "SRR2838702.bracken.report.txt:md5,3ca9ddfeb074bce0b9fd1e8b8b9c8443", - "SRR2838702.bracken.abundances.txt:md5,bfc7aea2ef689c21fdab164d29d2d57b", - [ - "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" - ] + "SRR2838702.bracken.report.txt:md5,3ca9ddfeb074bce0b9fd1e8b8b9c8443" ], - "timestamp": "2026-07-29T01:29:08.625794562", + "timestamp": "2026-07-30T00:28:11.754359711", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,13 +35,9 @@ }, "SRR2838702.bracken.tsv:md5,327dffe42a06c5819893b9043fc62f1a", "SRR2838702.kraken2.report.txt:md5,d883be153ee044e74a9504c128f20ccd", - "SRR2838702.bracken.report.txt:md5,2ed70b1d772694c9737e5c817efd2d97", - "SRR2838702.bracken.abundances.txt:md5,64fb9c79e36082acae54ead9cc8dcf83", - [ - "versions.yml:md5,ae267d8c8b147ab93417286c1cdcfd91" - ] + "SRR2838702.bracken.report.txt:md5,2ed70b1d772694c9737e5c817efd2d97" ], - "timestamp": "2026-07-29T01:32:44.608829119", + "timestamp": "2026-07-30T00:31:45.290162074", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/btyper3/tests/main.nf.test.snap b/modules/btyper3/tests/main.nf.test.snap index 17620e7da..656c5d4dc 100644 --- a/modules/btyper3/tests/main.nf.test.snap +++ b/modules/btyper3/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-29T01:32:06.398267795", + "timestamp": "2026-07-30T00:31:19.049715808", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-29T01:30:08.996194966", + "timestamp": "2026-07-30T00:29:27.177510154", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/busco/tests/main.nf.test.snap b/modules/busco/tests/main.nf.test.snap index ea4401a8f..93645a981 100644 --- a/modules/busco/tests/main.nf.test.snap +++ b/modules/busco/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-29T01:29:39.626561878", + "timestamp": "2026-07-30T00:28:37.885132821", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-29T01:29:00.704051991", + "timestamp": "2026-07-30T00:28:00.420520931", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm/lineagewf/tests/main.nf.test.snap b/modules/checkm/lineagewf/tests/main.nf.test.snap index 5cd23ea4d..13bdfe4da 100644 --- a/modules/checkm/lineagewf/tests/main.nf.test.snap +++ b/modules/checkm/lineagewf/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-29T01:37:46.356450791", + "timestamp": "2026-07-30T00:36:14.74113468", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-29T01:39:46.180001117", + "timestamp": "2026-07-30T00:38:33.400832662", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm2/predict/tests/main.nf.test.snap b/modules/checkm2/predict/tests/main.nf.test.snap index e4317f3f3..1e283e796 100644 --- a/modules/checkm2/predict/tests/main.nf.test.snap +++ b/modules/checkm2/predict/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-29T01:38:34.282334837", + "timestamp": "2026-07-30T00:36:57.527565395", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-29T01:33:33.954236979", + "timestamp": "2026-07-30T00:32:33.598548885", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clermontyping/tests/main.nf.test.snap b/modules/clermontyping/tests/main.nf.test.snap index 138cf4bf0..ef81ba646 100644 --- a/modules/clermontyping/tests/main.nf.test.snap +++ b/modules/clermontyping/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-29T01:29:31.436003132", + "timestamp": "2026-07-30T00:28:33.70061174", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-29T01:28:50.957786328", + "timestamp": "2026-07-30T00:27:52.24623652", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clonalframeml/tests/main.nf.test.snap b/modules/clonalframeml/tests/main.nf.test.snap index 7ac3faa34..e04371fdb 100644 --- a/modules/clonalframeml/tests/main.nf.test.snap +++ b/modules/clonalframeml/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-29T01:29:41.445652493", + "timestamp": "2026-07-30T00:28:40.41245868", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-29T01:31:00.864624347", + "timestamp": "2026-07-30T00:30:01.468282979", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/concat/tests/main.nf.test.snap b/modules/csvtk/concat/tests/main.nf.test.snap index d22f6ebd3..7f3cf7800 100644 --- a/modules/csvtk/concat/tests/main.nf.test.snap +++ b/modules/csvtk/concat/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-29T01:28:25.734452779", + "timestamp": "2026-07-30T00:27:41.403303919", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-29T01:28:38.021624805", + "timestamp": "2026-07-30T00:27:56.136849312", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/join/tests/main.nf.test.snap b/modules/csvtk/join/tests/main.nf.test.snap index d82bafa94..87bc3e4ff 100644 --- a/modules/csvtk/join/tests/main.nf.test.snap +++ b/modules/csvtk/join/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-29T01:28:28.735880068", + "timestamp": "2026-07-30T00:27:30.034340654", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-29T01:28:44.215441107", + "timestamp": "2026-07-30T00:27:44.265091067", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/deacon/filter/tests/main.nf.test.snap b/modules/deacon/filter/tests/main.nf.test.snap index fc237985d..182855ba3 100644 --- a/modules/deacon/filter/tests/main.nf.test.snap +++ b/modules/deacon/filter/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-29T01:29:57.869746208", + "timestamp": "2026-07-30T00:29:08.229204515", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-29T01:29:23.017586857", + "timestamp": "2026-07-30T00:28:32.499144526", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-29T01:28:49.029308216", + "timestamp": "2026-07-30T00:28:00.223385522", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/defensefinder/run/tests/main.nf.test.snap b/modules/defensefinder/run/tests/main.nf.test.snap index 8d6bfa001..7af560d42 100644 --- a/modules/defensefinder/run/tests/main.nf.test.snap +++ b/modules/defensefinder/run/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,96378138554cc40b07841aed5efb3e7d" ] ], - "timestamp": "2026-07-29T01:29:02.802693936", + "timestamp": "2026-07-30T00:28:20.926954356", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ectyper/tests/main.nf.test.snap b/modules/ectyper/tests/main.nf.test.snap index 01e3fa44d..013c43ed9 100644 --- a/modules/ectyper/tests/main.nf.test.snap +++ b/modules/ectyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-29T01:29:25.338543091", + "timestamp": "2026-07-30T00:28:33.264034136", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-29T01:28:46.893787037", + "timestamp": "2026-07-30T00:27:54.928583655", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/eggnog/mapper/tests/main.nf.test.snap b/modules/eggnog/mapper/tests/main.nf.test.snap index 2bab455ad..03f777ac1 100644 --- a/modules/eggnog/mapper/tests/main.nf.test.snap +++ b/modules/eggnog/mapper/tests/main.nf.test.snap @@ -8,12 +8,9 @@ "output_dir": "SRR2838702/tools/eggnog/", "process_name": "eggnog", "scope": "sample" - }, - [ - "versions.yml:md5,591b018c5d70f26267582a8932b0271d" - ] + } ], - "timestamp": "2026-07-29T01:42:09.932051896", + "timestamp": "2026-07-30T00:47:20.595133302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -28,12 +25,9 @@ "output_dir": "SRR2838702/tools/eggnog/", "process_name": "eggnog", "scope": "sample" - }, - [ - "versions.yml:md5,591b018c5d70f26267582a8932b0271d" - ] + } ], - "timestamp": "2026-07-29T01:46:27.638181705", + "timestamp": "2026-07-30T00:53:03.419968224", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/emmtyper/tests/main.nf.test.snap b/modules/emmtyper/tests/main.nf.test.snap index 1e31324a7..f5afb9a65 100644 --- a/modules/emmtyper/tests/main.nf.test.snap +++ b/modules/emmtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-29T01:28:53.180287944", + "timestamp": "2026-07-30T00:28:03.01572836", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-29T01:29:08.83918294", + "timestamp": "2026-07-30T00:28:18.255092721", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-29T01:28:37.398509688", + "timestamp": "2026-07-30T00:27:45.825260672", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/fastani/tests/main.nf.test.snap b/modules/fastani/tests/main.nf.test.snap index 37a726807..06b4e3aa8 100644 --- a/modules/fastani/tests/main.nf.test.snap +++ b/modules/fastani/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-29T01:28:29.889659595", + "timestamp": "2026-07-30T00:27:34.015623035", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-29T01:28:45.072480668", + "timestamp": "2026-07-30T00:27:48.801306304", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gamma/tests/main.nf.test.snap b/modules/gamma/tests/main.nf.test.snap index a72085baf..ca2dd8747 100644 --- a/modules/gamma/tests/main.nf.test.snap +++ b/modules/gamma/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-29T01:28:37.396500578", + "timestamp": "2026-07-30T00:27:41.680062691", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-29T01:28:53.37689059", + "timestamp": "2026-07-30T00:27:56.88346073", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genomedl/tests/main.nf.test.snap b/modules/genomedl/tests/main.nf.test.snap index eee2ed32e..e8e708e9d 100644 --- a/modules/genomedl/tests/main.nf.test.snap +++ b/modules/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-29T01:28:56.180701277", + "timestamp": "2026-07-30T00:28:04.222812434", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-29T01:28:37.710267022", + "timestamp": "2026-07-30T00:27:45.824303281", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-29T01:29:16.386057829", + "timestamp": "2026-07-30T00:28:22.029631151", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genotyphi/parse/tests/main.nf.test.snap b/modules/genotyphi/parse/tests/main.nf.test.snap index a0507db27..e092eb6e2 100644 --- a/modules/genotyphi/parse/tests/main.nf.test.snap +++ b/modules/genotyphi/parse/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,359680888d6e4e84784879e6e92c3439" ] ], - "timestamp": "2026-07-29T01:28:26.188471089", + "timestamp": "2026-07-30T00:27:35.802400406", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gigatyper/tests/main.nf.test.snap b/modules/gigatyper/tests/main.nf.test.snap index 37b9ddbe4..c1c9e5e88 100644 --- a/modules/gigatyper/tests/main.nf.test.snap +++ b/modules/gigatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ae98787b0c6ddf8f10515b895570a41a" ] ], - "timestamp": "2026-07-29T01:28:37.418545613", + "timestamp": "2026-07-30T00:27:50.37761076", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/gtdbtk/classifywf/tests/main.nf.test.snap index f4b1ac14f..4984b081b 100644 --- a/modules/gtdbtk/classifywf/tests/main.nf.test.snap +++ b/modules/gtdbtk/classifywf/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,7cb27f0b82d34e40565279ff91f60fda" ] ], - "timestamp": "2026-07-29T01:33:27.092172684", + "timestamp": "2026-07-30T00:32:22.666239454", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gubbins/tests/main.nf.test.snap b/modules/gubbins/tests/main.nf.test.snap index 01057c710..4ff212d93 100644 --- a/modules/gubbins/tests/main.nf.test.snap +++ b/modules/gubbins/tests/main.nf.test.snap @@ -9,12 +9,9 @@ "process_name": "gubbins", "scope": "run" }, - "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719", - [ - "versions.yml:md5,623c400503380dab143c222d825e55f6" - ] + "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719" ], - "timestamp": "2026-07-29T11:30:36.102332079", + "timestamp": "2026-07-30T00:28:31.765803438", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -30,12 +27,9 @@ "process_name": "gubbins", "scope": "run" }, - "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719", - [ - "versions.yml:md5,623c400503380dab143c222d825e55f6" - ] + "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719" ], - "timestamp": "2026-07-29T11:31:06.432688377", + "timestamp": "2026-07-30T00:29:33.303400589", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hicap/tests/main.nf.test.snap b/modules/hicap/tests/main.nf.test.snap index 964a09e54..19bff0a9b 100644 --- a/modules/hicap/tests/main.nf.test.snap +++ b/modules/hicap/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-29T01:29:41.345999565", + "timestamp": "2026-07-30T00:28:48.718747423", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-29T01:28:59.426370845", + "timestamp": "2026-07-30T00:28:09.002534693", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-29T01:30:55.41454133", + "timestamp": "2026-07-30T00:30:00.282551315", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-29T01:30:19.146421722", + "timestamp": "2026-07-30T00:29:25.433950184", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hpsuissero/tests/main.nf.test.snap b/modules/hpsuissero/tests/main.nf.test.snap index 9c7cc698d..5cf0914bc 100644 --- a/modules/hpsuissero/tests/main.nf.test.snap +++ b/modules/hpsuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-29T01:28:44.901139419", + "timestamp": "2026-07-30T00:27:50.398344313", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-29T01:28:28.575819213", + "timestamp": "2026-07-30T00:27:35.343292208", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/iqtree/tests/main.nf.test.snap b/modules/iqtree/tests/main.nf.test.snap index 2f99cee2c..32822f0a0 100644 --- a/modules/iqtree/tests/main.nf.test.snap +++ b/modules/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-29T01:28:53.673412493", + "timestamp": "2026-07-30T00:28:02.824648445", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-29T01:28:37.947807747", + "timestamp": "2026-07-30T00:27:46.468835351", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ismapper/tests/main.nf.test.snap b/modules/ismapper/tests/main.nf.test.snap index 577203826..49d4802a3 100644 --- a/modules/ismapper/tests/main.nf.test.snap +++ b/modules/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,bbe2280116459026bfc2304b2b6c0f5f" ] ], - "timestamp": "2026-07-29T01:29:29.79232796", + "timestamp": "2026-07-30T00:28:22.059010483", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kleborate/tests/main.nf.test.snap b/modules/kleborate/tests/main.nf.test.snap index 063f7bfa3..c7ca09cd5 100644 --- a/modules/kleborate/tests/main.nf.test.snap +++ b/modules/kleborate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9511fd36659702fc20722109151dca4b" ] ], - "timestamp": "2026-07-29T01:29:08.674898666", + "timestamp": "2026-07-30T00:28:03.978714127", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kraken2/tests/main.nf.test.snap b/modules/kraken2/tests/main.nf.test.snap index c2a6f0073..c7403a058 100644 --- a/modules/kraken2/tests/main.nf.test.snap +++ b/modules/kraken2/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-29T01:32:39.700156655", + "timestamp": "2026-07-30T00:31:40.440445989", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-29T01:29:02.901636556", + "timestamp": "2026-07-30T00:28:08.604957494", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/legsta/tests/main.nf.test.snap b/modules/legsta/tests/main.nf.test.snap index 0d4a4d07f..264038c8d 100644 --- a/modules/legsta/tests/main.nf.test.snap +++ b/modules/legsta/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1ea80a08aa0a9efc6d82ffa9e668ad6d" ] ], - "timestamp": "2026-07-29T01:28:26.639588521", + "timestamp": "2026-07-30T00:27:33.236665072", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/lissero/tests/main.nf.test.snap b/modules/lissero/tests/main.nf.test.snap index 10925ff96..4400634bb 100644 --- a/modules/lissero/tests/main.nf.test.snap +++ b/modules/lissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-29T01:28:49.53199812", + "timestamp": "2026-07-30T00:27:49.542026847", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-29T01:28:31.309469065", + "timestamp": "2026-07-30T00:27:32.933525251", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mash/dist/tests/main.nf.test.snap b/modules/mash/dist/tests/main.nf.test.snap index 26a22a31d..922b5985d 100644 --- a/modules/mash/dist/tests/main.nf.test.snap +++ b/modules/mash/dist/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-29T01:28:42.959541898", + "timestamp": "2026-07-30T00:27:45.316719659", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-29T01:28:27.866033658", + "timestamp": "2026-07-30T00:27:30.975255211", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mashtree/tests/main.nf.test.snap b/modules/mashtree/tests/main.nf.test.snap index f828342ba..0af15d148 100644 --- a/modules/mashtree/tests/main.nf.test.snap +++ b/modules/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,6d51bcb025e39e73864f2236b1ce99e9" ] ], - "timestamp": "2026-07-29T01:28:33.892279973", + "timestamp": "2026-07-30T00:27:34.300206931", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mcroni/tests/main.nf.test.snap b/modules/mcroni/tests/main.nf.test.snap index 146153a4d..46fae15d9 100644 --- a/modules/mcroni/tests/main.nf.test.snap +++ b/modules/mcroni/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-29T01:28:52.637121097", + "timestamp": "2026-07-30T00:27:47.350368123", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-29T01:28:35.605702524", + "timestamp": "2026-07-30T00:27:30.714177546", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/meningotype/tests/main.nf.test.snap b/modules/meningotype/tests/main.nf.test.snap index 3a595a1d8..11d8672cb 100644 --- a/modules/meningotype/tests/main.nf.test.snap +++ b/modules/meningotype/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-29T01:28:41.488960841", + "timestamp": "2026-07-30T00:27:55.96254851", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-29T01:28:26.183236981", + "timestamp": "2026-07-30T00:27:38.424258563", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/merlin/dist/tests/main.nf.test.snap b/modules/merlin/dist/tests/main.nf.test.snap index 0e7acddf6..7317ef9d4 100644 --- a/modules/merlin/dist/tests/main.nf.test.snap +++ b/modules/merlin/dist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-29T01:29:36.578914755", + "timestamp": "2026-07-30T00:28:57.416946521", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-29T01:30:57.258068201", + "timestamp": "2026-07-30T00:30:16.561889489", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/midas/species/tests/main.nf.test.snap b/modules/midas/species/tests/main.nf.test.snap index 799a33167..2da6bfe04 100644 --- a/modules/midas/species/tests/main.nf.test.snap +++ b/modules/midas/species/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-29T01:35:16.988424548", + "timestamp": "2026-07-30T00:34:37.316406256", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-29T01:36:15.146887371", + "timestamp": "2026-07-30T00:35:28.238972692", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mlst/tests/main.nf.test.snap b/modules/mlst/tests/main.nf.test.snap index bddff9fa9..bb6445264 100644 --- a/modules/mlst/tests/main.nf.test.snap +++ b/modules/mlst/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6515f9242cdb83b9c720f39ce67a528f" ] ], - "timestamp": "2026-07-29T01:28:30.214334872", + "timestamp": "2026-07-30T00:27:45.810778893", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mobsuite/recon/tests/main.nf.test.snap b/modules/mobsuite/recon/tests/main.nf.test.snap index 526fc5ffa..fe546d9de 100644 --- a/modules/mobsuite/recon/tests/main.nf.test.snap +++ b/modules/mobsuite/recon/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-29T01:32:39.788411473", + "timestamp": "2026-07-30T00:31:45.827171744", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -40,7 +40,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-29T01:31:32.174679544", + "timestamp": "2026-07-30T00:30:41.901408002", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-29T01:29:56.247980884", + "timestamp": "2026-07-30T00:29:10.044478174", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mykrobe/predict/tests/main.nf.test.snap b/modules/mykrobe/predict/tests/main.nf.test.snap index 981a3a4c8..600eaf1f7 100644 --- a/modules/mykrobe/predict/tests/main.nf.test.snap +++ b/modules/mykrobe/predict/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,3756fdfbed62cef8782098468ef3da9d" ] ], - "timestamp": "2026-07-29T01:28:37.396382827", + "timestamp": "2026-07-30T00:27:36.523004377", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ngmaster/tests/main.nf.test.snap b/modules/ngmaster/tests/main.nf.test.snap index 70486d37b..7579c3c2c 100644 --- a/modules/ngmaster/tests/main.nf.test.snap +++ b/modules/ngmaster/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-29T01:28:32.227397767", + "timestamp": "2026-07-30T00:27:41.353453999", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-29T01:28:55.706135945", + "timestamp": "2026-07-30T00:28:04.721327371", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/nohuman/run/tests/main.nf.test.snap b/modules/nohuman/run/tests/main.nf.test.snap index 3d4bede4c..4e91224cd 100644 --- a/modules/nohuman/run/tests/main.nf.test.snap +++ b/modules/nohuman/run/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-29T01:40:15.078503284", + "timestamp": "2026-07-30T00:39:14.923721815", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-29T01:43:54.729970861", + "timestamp": "2026-07-30T00:43:19.706825284", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-29T01:35:29.001683385", + "timestamp": "2026-07-30T00:34:26.778722457", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/panaroo/run/tests/main.nf.test.snap b/modules/panaroo/run/tests/main.nf.test.snap index 1ccd7bcce..00ac91f03 100644 --- a/modules/panaroo/run/tests/main.nf.test.snap +++ b/modules/panaroo/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e6a0f1e191dcfb92fab2a7d68063c31d" ] ], - "timestamp": "2026-07-29T01:30:14.863586619", + "timestamp": "2026-07-30T00:29:25.379571834", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pasty/tests/main.nf.test.snap b/modules/pasty/tests/main.nf.test.snap index 8e2887b85..05020df86 100644 --- a/modules/pasty/tests/main.nf.test.snap +++ b/modules/pasty/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258" ], - "timestamp": "2026-07-29T23:14:45.169553619", + "timestamp": "2026-07-30T00:27:38.829262086", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pbptyper/tests/main.nf.test.snap b/modules/pbptyper/tests/main.nf.test.snap index 4c1b34378..7ae892c65 100644 --- a/modules/pbptyper/tests/main.nf.test.snap +++ b/modules/pbptyper/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967" ], - "timestamp": "2026-07-29T21:59:05.002681726", + "timestamp": "2026-07-30T00:28:15.874910363", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/phispy/tests/main.nf.test.snap b/modules/phispy/tests/main.nf.test.snap index 55da66ef7..1d5f2afd3 100644 --- a/modules/phispy/tests/main.nf.test.snap +++ b/modules/phispy/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,97542c4eb1d90b2b0a0375c916b75dc5" ] ], - "timestamp": "2026-07-29T01:30:56.561524725", + "timestamp": "2026-07-30T00:29:58.59773508", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pirate/tests/main.nf.test.snap b/modules/pirate/tests/main.nf.test.snap index a58376b56..8c2cb043a 100644 --- a/modules/pirate/tests/main.nf.test.snap +++ b/modules/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,ce4d40e2b87e2e5cac6e755fcb0c023b" ] ], - "timestamp": "2026-07-29T01:31:40.088702729", + "timestamp": "2026-07-30T00:30:44.697742266", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/plasmidfinder/tests/main.nf.test.snap b/modules/plasmidfinder/tests/main.nf.test.snap index 45c44dfbf..04311d63f 100644 --- a/modules/plasmidfinder/tests/main.nf.test.snap +++ b/modules/plasmidfinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-29T01:29:01.42436456", + "timestamp": "2026-07-30T00:29:08.915528222", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-29T01:29:25.033686013", + "timestamp": "2026-07-30T00:29:29.478069468", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pneumocat/tests/main.nf.test.snap b/modules/pneumocat/tests/main.nf.test.snap index 123ebd711..3667c7d48 100644 --- a/modules/pneumocat/tests/main.nf.test.snap +++ b/modules/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf" ] ], - "timestamp": "2026-07-29T01:29:13.655966628", + "timestamp": "2026-07-30T00:29:21.57152769", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/prokka/tests/main.nf.test.snap b/modules/prokka/tests/main.nf.test.snap index 4f8cf62be..b51ba1760 100644 --- a/modules/prokka/tests/main.nf.test.snap +++ b/modules/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-29T01:29:47.874375257", + "timestamp": "2026-07-30T00:29:52.218047901", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-29T01:30:20.662561693", + "timestamp": "2026-07-30T00:30:22.356426243", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-29T01:31:09.500747676", + "timestamp": "2026-07-30T00:31:06.553215483", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/quast/tests/main.nf.test.snap b/modules/quast/tests/main.nf.test.snap index c8d7e24fd..db9f5c254 100644 --- a/modules/quast/tests/main.nf.test.snap +++ b/modules/quast/tests/main.nf.test.snap @@ -9,12 +9,9 @@ "process_name": "quast", "scope": "sample" }, - "SRR2838702.tsv:md5,79fa78c69537697be5eee30f630833d7", - [ - "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" - ] + "SRR2838702.tsv:md5,79fa78c69537697be5eee30f630833d7" ], - "timestamp": "2026-07-29T01:30:02.385132653", + "timestamp": "2026-07-30T00:30:03.390878259", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -30,12 +27,9 @@ "process_name": "quast", "scope": "sample" }, - "SRR2838702.tsv:md5,a02f798379d9982810a198ec9b389079", - [ - "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" - ] + "SRR2838702.tsv:md5,a02f798379d9982810a198ec9b389079" ], - "timestamp": "2026-07-29T01:29:39.532960005", + "timestamp": "2026-07-30T00:29:44.261319001", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -51,12 +45,9 @@ "process_name": "quast", "scope": "sample" }, - "SRR2838702.tsv:md5,2e31a6f1283ca3a7aa253ab81266b85f", - [ - "versions.yml:md5,951ec08af8a1a4466340060a5c95b6c5" - ] + "SRR2838702.tsv:md5,2e31a6f1283ca3a7aa253ab81266b85f" ], - "timestamp": "2026-07-29T01:29:14.30005886", + "timestamp": "2026-07-30T00:29:21.397650785", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/heatmap/tests/main.nf.test.snap b/modules/rgi/heatmap/tests/main.nf.test.snap index 617be3ff3..222be3b27 100644 --- a/modules/rgi/heatmap/tests/main.nf.test.snap +++ b/modules/rgi/heatmap/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,85fd687a901fef3c05e188fe49391c68" ] ], - "timestamp": "2026-07-29T01:29:19.004197858", + "timestamp": "2026-07-30T00:29:26.318079261", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/main/tests/main.nf.test.snap b/modules/rgi/main/tests/main.nf.test.snap index 81262c018..12bbdba04 100644 --- a/modules/rgi/main/tests/main.nf.test.snap +++ b/modules/rgi/main/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-29T01:30:14.523232332", + "timestamp": "2026-07-30T00:30:22.913079927", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-29T01:32:51.787211419", + "timestamp": "2026-07-30T00:32:54.333765302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-29T01:31:32.600476615", + "timestamp": "2026-07-30T00:31:37.128227456", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/roary/tests/main.nf.test.snap b/modules/roary/tests/main.nf.test.snap index 1c1045866..17d158bda 100644 --- a/modules/roary/tests/main.nf.test.snap +++ b/modules/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,80c99c1b38b33ebcb7925eabba7ca2eb" ] ], - "timestamp": "2026-07-29T01:30:43.478592884", + "timestamp": "2026-07-30T00:30:49.42146625", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sccmec/tests/main.nf.test.snap b/modules/sccmec/tests/main.nf.test.snap index 5653a541e..24c32376d 100644 --- a/modules/sccmec/tests/main.nf.test.snap +++ b/modules/sccmec/tests/main.nf.test.snap @@ -12,7 +12,7 @@ "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-29T21:36:46.280663291", + "timestamp": "2026-07-30T00:29:24.986631049", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -31,7 +31,7 @@ "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-29T21:36:55.946499331", + "timestamp": "2026-07-30T00:29:43.649817563", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/scoary/tests/main.nf.test.snap b/modules/scoary/tests/main.nf.test.snap index 058f73ae1..9f9471bed 100644 --- a/modules/scoary/tests/main.nf.test.snap +++ b/modules/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,f8f8a2300f84de4e8184c9dd33579ccd" ] ], - "timestamp": "2026-07-29T01:29:13.87691542", + "timestamp": "2026-07-30T00:29:22.425655254", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seqsero2/tests/main.nf.test.snap b/modules/seqsero2/tests/main.nf.test.snap index 88ae69e4a..927eacf2f 100644 --- a/modules/seqsero2/tests/main.nf.test.snap +++ b/modules/seqsero2/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-29T01:29:32.01873251", + "timestamp": "2026-07-30T00:29:37.098376092", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-29T01:29:15.566965302", + "timestamp": "2026-07-30T00:29:22.232803566", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seroba/run/tests/main.nf.test.snap b/modules/seroba/run/tests/main.nf.test.snap index d4cc4bf6a..d661a554d 100644 --- a/modules/seroba/run/tests/main.nf.test.snap +++ b/modules/seroba/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,e485bb335ccae3f5e5f24f35690633d3" ] ], - "timestamp": "2026-07-29T01:29:52.632361366", + "timestamp": "2026-07-30T00:29:55.428514816", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigapass/tests/main.nf.test.snap b/modules/shigapass/tests/main.nf.test.snap index 2b9d684e7..e0ed2daa6 100644 --- a/modules/shigapass/tests/main.nf.test.snap +++ b/modules/shigapass/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-29T01:29:34.756318038", + "timestamp": "2026-07-30T00:29:48.360417064", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-29T01:30:00.877488575", + "timestamp": "2026-07-30T00:30:13.008214619", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigatyper/tests/main.nf.test.snap b/modules/shigatyper/tests/main.nf.test.snap index 69a3f10ae..8c8d2e08f 100644 --- a/modules/shigatyper/tests/main.nf.test.snap +++ b/modules/shigatyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,5546505c7719718340a0cd98ece587d8" ] ], - "timestamp": "2026-07-29T01:29:27.06297208", + "timestamp": "2026-07-30T00:29:48.300878513", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigeifinder/tests/main.nf.test.snap b/modules/shigeifinder/tests/main.nf.test.snap index e2207d673..a960599a7 100644 --- a/modules/shigeifinder/tests/main.nf.test.snap +++ b/modules/shigeifinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-29T01:29:40.833944402", + "timestamp": "2026-07-30T00:29:58.546208686", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-29T01:29:25.24104086", + "timestamp": "2026-07-30T00:29:45.79707681", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sistr/tests/main.nf.test.snap b/modules/sistr/tests/main.nf.test.snap index 1159d7786..08a03b13a 100644 --- a/modules/sistr/tests/main.nf.test.snap +++ b/modules/sistr/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-29T21:42:14.544418614", + "timestamp": "2026-07-30T00:30:16.287630692", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-29T21:42:33.228698437", + "timestamp": "2026-07-30T00:30:53.487750678", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/core/tests/main.nf.test.snap b/modules/snippy/core/tests/main.nf.test.snap index 104ab9120..3b8ec10ca 100644 --- a/modules/snippy/core/tests/main.nf.test.snap +++ b/modules/snippy/core/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,af05caa4daa181fbe9d7bf82d3383d93" ] ], - "timestamp": "2026-07-29T11:32:47.889364457", + "timestamp": "2026-07-30T00:30:13.481417038", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/run/tests/main.nf.test.snap b/modules/snippy/run/tests/main.nf.test.snap index 0a03b79de..00695be1b 100644 --- a/modules/snippy/run/tests/main.nf.test.snap +++ b/modules/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-29T11:33:22.643578596", + "timestamp": "2026-07-30T00:31:10.016003134", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-29T11:33:02.588615911", + "timestamp": "2026-07-30T00:30:37.245702654", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snpdists/tests/main.nf.test.snap b/modules/snpdists/tests/main.nf.test.snap index 6040dcff2..c74b7625b 100644 --- a/modules/snpdists/tests/main.nf.test.snap +++ b/modules/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,944b6ecf9bf11c38b608ae08b36d5e2d" ] ], - "timestamp": "2026-07-29T01:29:38.075792054", + "timestamp": "2026-07-30T00:30:18.463312289", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/spatyper/tests/main.nf.test.snap b/modules/spatyper/tests/main.nf.test.snap index 5718e7f24..5dfa49ac5 100644 --- a/modules/spatyper/tests/main.nf.test.snap +++ b/modules/spatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-29T01:30:05.767014154", + "timestamp": "2026-07-30T00:30:43.658738231", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-29T01:29:45.843982744", + "timestamp": "2026-07-30T00:30:26.055766212", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap index 94a5bf1fb..76f9c1e40 100644 --- a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap +++ b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-29T01:31:42.097451028", + "timestamp": "2026-07-30T00:32:21.642160814", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-29T01:30:53.448245388", + "timestamp": "2026-07-30T00:31:33.317790804", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ssuissero/tests/main.nf.test.snap b/modules/ssuissero/tests/main.nf.test.snap index 2d24a5872..54612542c 100644 --- a/modules/ssuissero/tests/main.nf.test.snap +++ b/modules/ssuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-29T01:29:42.832734695", + "timestamp": "2026-07-30T00:30:25.226392647", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-29T01:29:56.850525477", + "timestamp": "2026-07-30T00:30:37.564989688", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphopiasccmec/tests/main.nf.test.snap b/modules/staphopiasccmec/tests/main.nf.test.snap index 62782f018..4a03e4a07 100644 --- a/modules/staphopiasccmec/tests/main.nf.test.snap +++ b/modules/staphopiasccmec/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-29T01:29:44.925199169", + "timestamp": "2026-07-30T00:30:27.458716495", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-29T01:29:59.641091224", + "timestamp": "2026-07-30T00:30:40.137500387", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphscan/tests/main.nf.test.snap b/modules/staphscan/tests/main.nf.test.snap index 038f09cca..58851d987 100644 --- a/modules/staphscan/tests/main.nf.test.snap +++ b/modules/staphscan/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,251f3e6b35be5f660d5fc8bc8456bde6" ] ], - "timestamp": "2026-07-29T01:30:00.265720929", + "timestamp": "2026-07-30T00:30:43.880114172", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stecfinder/tests/main.nf.test.snap b/modules/stecfinder/tests/main.nf.test.snap index 56c4318d3..afaac69ff 100644 --- a/modules/stecfinder/tests/main.nf.test.snap +++ b/modules/stecfinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-29T01:30:20.622055724", + "timestamp": "2026-07-30T00:30:56.074503103", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-29T01:30:05.008808748", + "timestamp": "2026-07-30T00:30:44.761262358", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-29T01:29:50.297484471", + "timestamp": "2026-07-30T00:30:31.907468861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stxtyper/tests/main.nf.test.snap b/modules/stxtyper/tests/main.nf.test.snap index 33726ead9..7129038d8 100644 --- a/modules/stxtyper/tests/main.nf.test.snap +++ b/modules/stxtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9ebd9c1f28e4ce3da541f707abeaa52" ] ], - "timestamp": "2026-07-29T01:29:55.127321385", + "timestamp": "2026-07-30T00:30:40.993582478", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sylph/profile/tests/main.nf.test.snap b/modules/sylph/profile/tests/main.nf.test.snap index 62aeafd38..f9ba65670 100644 --- a/modules/sylph/profile/tests/main.nf.test.snap +++ b/modules/sylph/profile/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-29T01:31:58.409657025", + "timestamp": "2026-07-30T00:32:47.326426676", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-29T01:30:47.804158618", + "timestamp": "2026-07-30T00:31:38.283348181", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/collate/tests/main.nf.test.snap b/modules/tbprofiler/collate/tests/main.nf.test.snap index b7837dead..e57985f5e 100644 --- a/modules/tbprofiler/collate/tests/main.nf.test.snap +++ b/modules/tbprofiler/collate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,3c3d5fbb783c5cb96c154683bf56699a" ] ], - "timestamp": "2026-07-29T01:29:58.26631694", + "timestamp": "2026-07-30T00:31:01.086481659", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/profile/tests/main.nf.test.snap b/modules/tbprofiler/profile/tests/main.nf.test.snap index 4d060180e..b0d5bf276 100644 --- a/modules/tbprofiler/profile/tests/main.nf.test.snap +++ b/modules/tbprofiler/profile/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-29T01:30:49.127861115", + "timestamp": "2026-07-30T00:31:47.72057877", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-29T01:31:43.549826966", + "timestamp": "2026-07-30T00:32:41.836741059", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-29T01:32:50.311768437", + "timestamp": "2026-07-30T00:33:50.46224948", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/traitar/run/tests/main.nf.test.snap b/modules/traitar/run/tests/main.nf.test.snap index 311c12e58..9be570d56 100644 --- a/modules/traitar/run/tests/main.nf.test.snap +++ b/modules/traitar/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-29T01:35:54.478734701", + "timestamp": "2026-07-30T00:36:44.596384058", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-29T01:41:12.495040022", + "timestamp": "2026-07-30T00:42:30.217169799", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abricate/tests/main.nf.test.snap b/subworkflows/abricate/tests/main.nf.test.snap index da3b3e01e..b5749f58e 100644 --- a/subworkflows/abricate/tests/main.nf.test.snap +++ b/subworkflows/abricate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-07-29T01:30:06.743112087", + "timestamp": "2026-07-30T00:31:30.423869908", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abritamr/tests/main.nf.test.snap b/subworkflows/abritamr/tests/main.nf.test.snap index aaed94a18..5d26353d8 100644 --- a/subworkflows/abritamr/tests/main.nf.test.snap +++ b/subworkflows/abritamr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-07-29T01:34:15.196675503", + "timestamp": "2026-07-30T00:35:37.041063985", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/agrvate/tests/main.nf.test.snap b/subworkflows/agrvate/tests/main.nf.test.snap index bce6ff19d..4da631644 100644 --- a/subworkflows/agrvate/tests/main.nf.test.snap +++ b/subworkflows/agrvate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-29T01:30:16.45924252", + "timestamp": "2026-07-30T00:31:33.007429645", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/amrfinderplus/tests/main.nf.test.snap b/subworkflows/amrfinderplus/tests/main.nf.test.snap index 5b73eac55..c1a2e98ec 100644 --- a/subworkflows/amrfinderplus/tests/main.nf.test.snap +++ b/subworkflows/amrfinderplus/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-07-29T01:30:24.02145379", + "timestamp": "2026-07-30T00:31:45.513803737", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ariba/tests/main.nf.test.snap b/subworkflows/ariba/tests/main.nf.test.snap index b02ffcba9..21b1b5403 100644 --- a/subworkflows/ariba/tests/main.nf.test.snap +++ b/subworkflows/ariba/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6" ] ], - "timestamp": "2026-07-29T01:37:29.525427341", + "timestamp": "2026-07-30T00:38:28.71671844", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap index da343ba40..d0f36818a 100644 --- a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap +++ b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e46de3078794860a978e2dd0b390c27c" ] ], - "timestamp": "2026-07-29T01:31:33.92428099", + "timestamp": "2026-07-30T00:33:07.050007635", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bakta/tests/main.nf.test.snap b/subworkflows/bakta/tests/main.nf.test.snap index 4a2892e78..5ad86605b 100644 --- a/subworkflows/bakta/tests/main.nf.test.snap +++ b/subworkflows/bakta/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-29T01:34:21.723312817", + "timestamp": "2026-07-30T00:35:58.969384589", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastn/tests/main.nf.test.snap b/subworkflows/blastn/tests/main.nf.test.snap index 2c2ca7dc2..a2deb8361 100644 --- a/subworkflows/blastn/tests/main.nf.test.snap +++ b/subworkflows/blastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-29T01:30:25.346784151", + "timestamp": "2026-07-30T00:32:05.903153684", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastp/tests/main.nf.test.snap b/subworkflows/blastp/tests/main.nf.test.snap index 9cd6052f9..2d6d94aa1 100644 --- a/subworkflows/blastp/tests/main.nf.test.snap +++ b/subworkflows/blastp/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-29T01:30:33.502856524", + "timestamp": "2026-07-30T00:32:07.283334472", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastx/tests/main.nf.test.snap b/subworkflows/blastx/tests/main.nf.test.snap index 082bc4476..0a45e5237 100644 --- a/subworkflows/blastx/tests/main.nf.test.snap +++ b/subworkflows/blastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-29T01:30:34.326686053", + "timestamp": "2026-07-30T00:32:14.674402011", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/btyper3/tests/main.nf.test.snap b/subworkflows/btyper3/tests/main.nf.test.snap index 8c7b6a24c..351d1d225 100644 --- a/subworkflows/btyper3/tests/main.nf.test.snap +++ b/subworkflows/btyper3/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-07-29T01:32:20.254687553", + "timestamp": "2026-07-30T00:34:08.956730486", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/busco/tests/main.nf.test.snap b/subworkflows/busco/tests/main.nf.test.snap index 87923e638..a68ba71b3 100644 --- a/subworkflows/busco/tests/main.nf.test.snap +++ b/subworkflows/busco/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-07-29T01:31:00.588487004", + "timestamp": "2026-07-30T00:32:53.545050122", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm/tests/main.nf.test.snap b/subworkflows/checkm/tests/main.nf.test.snap index 925647384..1714a1af2 100644 --- a/subworkflows/checkm/tests/main.nf.test.snap +++ b/subworkflows/checkm/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-07-29T01:32:49.469775023", + "timestamp": "2026-07-30T00:34:40.244690509", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm2/tests/main.nf.test.snap b/subworkflows/checkm2/tests/main.nf.test.snap index d8708eef0..00c8214f7 100644 --- a/subworkflows/checkm2/tests/main.nf.test.snap +++ b/subworkflows/checkm2/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-07-29T01:35:39.175475676", + "timestamp": "2026-07-30T00:36:58.648228101", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clermontyping/tests/main.nf.test.snap b/subworkflows/clermontyping/tests/main.nf.test.snap index 36614c5a3..225cbc362 100644 --- a/subworkflows/clermontyping/tests/main.nf.test.snap +++ b/subworkflows/clermontyping/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-07-29T01:31:08.906240322", + "timestamp": "2026-07-30T00:33:17.856793542", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clonalframeml/tests/main.nf.test.snap b/subworkflows/clonalframeml/tests/main.nf.test.snap index e71e0e3dd..f3a052ef5 100644 --- a/subworkflows/clonalframeml/tests/main.nf.test.snap +++ b/subworkflows/clonalframeml/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,77f64a20eeab9152a61953ec5203b926" ] ], - "timestamp": "2026-07-29T01:32:01.093772558", + "timestamp": "2026-07-30T00:34:05.952322455", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/deacon/tests/main.nf.test.snap b/subworkflows/deacon/tests/main.nf.test.snap index 261708302..07077a745 100644 --- a/subworkflows/deacon/tests/main.nf.test.snap +++ b/subworkflows/deacon/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,9d3e1c1b5110e0048698861366ed5151" ] ], - "timestamp": "2026-07-29T01:31:09.405549548", + "timestamp": "2026-07-30T00:33:19.720003517", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/defensefinder/tests/main.nf.test.snap b/subworkflows/defensefinder/tests/main.nf.test.snap index e37849cdb..98bf38c5f 100644 --- a/subworkflows/defensefinder/tests/main.nf.test.snap +++ b/subworkflows/defensefinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,cac1e24b64c152890e712ac2077fc111" ] ], - "timestamp": "2026-07-29T01:31:51.41904158", + "timestamp": "2026-07-30T00:34:00.925711291", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ectyper/tests/main.nf.test.snap b/subworkflows/ectyper/tests/main.nf.test.snap index fc0a03085..41d710094 100644 --- a/subworkflows/ectyper/tests/main.nf.test.snap +++ b/subworkflows/ectyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-29T01:31:21.682749302", + "timestamp": "2026-07-30T00:33:39.573436078", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/eggnog/tests/main.nf.test.snap b/subworkflows/eggnog/tests/main.nf.test.snap index 1fd64899c..8a7df7b95 100644 --- a/subworkflows/eggnog/tests/main.nf.test.snap +++ b/subworkflows/eggnog/tests/main.nf.test.snap @@ -8,12 +8,9 @@ "output_dir": "SRR2838702/tools/eggnog/", "process_name": "eggnog", "scope": "sample" - }, - [ - "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" - ] + } ], - "timestamp": "2026-07-29T01:45:10.522762836", + "timestamp": "2026-07-30T00:54:55.63046983", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/emmtyper/tests/main.nf.test.snap b/subworkflows/emmtyper/tests/main.nf.test.snap index 654706fb5..1fd058f77 100644 --- a/subworkflows/emmtyper/tests/main.nf.test.snap +++ b/subworkflows/emmtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-29T01:30:58.588619788", + "timestamp": "2026-07-30T00:33:20.599767449", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/fastani/tests/main.nf.test.snap b/subworkflows/fastani/tests/main.nf.test.snap index 9e4ad8caf..bf1698868 100644 --- a/subworkflows/fastani/tests/main.nf.test.snap +++ b/subworkflows/fastani/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-29T01:31:00.320189923", + "timestamp": "2026-07-30T00:33:23.274314219", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gamma/tests/main.nf.test.snap b/subworkflows/gamma/tests/main.nf.test.snap index 40a7222d3..fe5d6b695 100644 --- a/subworkflows/gamma/tests/main.nf.test.snap +++ b/subworkflows/gamma/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-07-29T01:31:03.007160677", + "timestamp": "2026-07-30T00:33:40.984944802", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genomedl/tests/main.nf.test.snap b/subworkflows/genomedl/tests/main.nf.test.snap index 70b3c7cec..cf44cb71e 100644 --- a/subworkflows/genomedl/tests/main.nf.test.snap +++ b/subworkflows/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-29T01:31:22.747968011", + "timestamp": "2026-07-30T00:33:56.13524619", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-29T01:31:39.120738784", + "timestamp": "2026-07-30T00:34:09.299195954", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-29T01:31:05.511427719", + "timestamp": "2026-07-30T00:33:42.265850529", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genotyphi/tests/main.nf.test.snap b/subworkflows/genotyphi/tests/main.nf.test.snap index 853f5f278..c478e6c1e 100644 --- a/subworkflows/genotyphi/tests/main.nf.test.snap +++ b/subworkflows/genotyphi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-07-29T01:31:15.456870595", + "timestamp": "2026-07-30T00:34:00.410523002", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gigatyper/tests/main.nf.test.snap b/subworkflows/gigatyper/tests/main.nf.test.snap index e9064eabb..be3962e14 100644 --- a/subworkflows/gigatyper/tests/main.nf.test.snap +++ b/subworkflows/gigatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-29T01:31:22.433297539", + "timestamp": "2026-07-30T00:34:06.395619732", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gtdb/tests/main.nf.test.snap b/subworkflows/gtdb/tests/main.nf.test.snap index 4afaa9403..b33ee9ab3 100644 --- a/subworkflows/gtdb/tests/main.nf.test.snap +++ b/subworkflows/gtdb/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-29T01:36:17.045906766", + "timestamp": "2026-07-30T00:38:51.017195314", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gubbins/tests/main.nf.test.snap b/subworkflows/gubbins/tests/main.nf.test.snap index 7716e9b63..b8bd44314 100644 --- a/subworkflows/gubbins/tests/main.nf.test.snap +++ b/subworkflows/gubbins/tests/main.nf.test.snap @@ -10,9 +10,6 @@ "scope": "run" }, "portiera.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719", - [ - "versions.yml:md5,99bfa6c29403a77acf3449315065c245" - ], { "id": "core-snp.masked.distance-snpdists", "logs_dir": "snpdists-masked/logs/", @@ -26,7 +23,7 @@ "versions.yml:md5,a8d93e0d6a006b32c088567301fe66c4" ] ], - "timestamp": "2026-07-29T11:30:36.911261125", + "timestamp": "2026-07-30T00:34:44.058417638", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hicap/tests/main.nf.test.snap b/subworkflows/hicap/tests/main.nf.test.snap index c735fc49e..333f39254 100644 --- a/subworkflows/hicap/tests/main.nf.test.snap +++ b/subworkflows/hicap/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-29T01:31:38.216821349", + "timestamp": "2026-07-30T00:34:25.138723306", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hpsuissero/tests/main.nf.test.snap b/subworkflows/hpsuissero/tests/main.nf.test.snap index e219538a5..92460192c 100644 --- a/subworkflows/hpsuissero/tests/main.nf.test.snap +++ b/subworkflows/hpsuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-29T01:31:17.100346315", + "timestamp": "2026-07-30T00:34:19.520796177", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/iqtree/tests/main.nf.test.snap b/subworkflows/iqtree/tests/main.nf.test.snap index 5cb5779a7..77df8b94e 100644 --- a/subworkflows/iqtree/tests/main.nf.test.snap +++ b/subworkflows/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f" ] ], - "timestamp": "2026-07-29T01:31:20.642269187", + "timestamp": "2026-07-30T00:34:29.238796807", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ismapper/tests/main.nf.test.snap b/subworkflows/ismapper/tests/main.nf.test.snap index cbad8b78b..68b798af7 100644 --- a/subworkflows/ismapper/tests/main.nf.test.snap +++ b/subworkflows/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-29T01:32:32.308738036", + "timestamp": "2026-07-30T00:35:39.372749302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kleborate/tests/main.nf.test.snap b/subworkflows/kleborate/tests/main.nf.test.snap index ac77cc2ad..f806ba64b 100644 --- a/subworkflows/kleborate/tests/main.nf.test.snap +++ b/subworkflows/kleborate/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-29T01:31:54.671281793", + "timestamp": "2026-07-30T00:35:26.770609969", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kraken2/tests/main.nf.test.snap b/subworkflows/kraken2/tests/main.nf.test.snap index b7a6702b2..69d88f093 100644 --- a/subworkflows/kraken2/tests/main.nf.test.snap +++ b/subworkflows/kraken2/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-29T01:31:58.539251149", + "timestamp": "2026-07-30T00:35:30.694078732", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/legsta/tests/main.nf.test.snap b/subworkflows/legsta/tests/main.nf.test.snap index f77204239..9e9443a60 100644 --- a/subworkflows/legsta/tests/main.nf.test.snap +++ b/subworkflows/legsta/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-29T01:31:42.192658084", + "timestamp": "2026-07-30T00:35:06.120555112", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/lissero/tests/main.nf.test.snap b/subworkflows/lissero/tests/main.nf.test.snap index ba733dbc3..3aa037bed 100644 --- a/subworkflows/lissero/tests/main.nf.test.snap +++ b/subworkflows/lissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-29T01:31:45.264431252", + "timestamp": "2026-07-30T00:35:10.201863302", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashdist/tests/main.nf.test.snap b/subworkflows/mashdist/tests/main.nf.test.snap index d84657ba3..e881118d1 100644 --- a/subworkflows/mashdist/tests/main.nf.test.snap +++ b/subworkflows/mashdist/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,fa387a5652585c181be4884eb12f37b0" ] ], - "timestamp": "2026-07-29T01:31:43.70879255", + "timestamp": "2026-07-30T00:35:22.399281695", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashtree/tests/main.nf.test.snap b/subworkflows/mashtree/tests/main.nf.test.snap index 82886928a..d276b01b1 100644 --- a/subworkflows/mashtree/tests/main.nf.test.snap +++ b/subworkflows/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8cd0c9b6f670d5ae21fda6592e85d32" ] ], - "timestamp": "2026-07-29T01:31:44.050773236", + "timestamp": "2026-07-30T00:35:41.654238607", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mcroni/tests/main.nf.test.snap b/subworkflows/mcroni/tests/main.nf.test.snap index 16625f6b1..ab5340a98 100644 --- a/subworkflows/mcroni/tests/main.nf.test.snap +++ b/subworkflows/mcroni/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,6eecf339ecef6511e62beca33a4b3fc6" ] ], - "timestamp": "2026-07-29T01:32:01.241013814", + "timestamp": "2026-07-30T00:36:00.175515475", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/meningotype/tests/main.nf.test.snap b/subworkflows/meningotype/tests/main.nf.test.snap index d30b986c3..4541103bf 100644 --- a/subworkflows/meningotype/tests/main.nf.test.snap +++ b/subworkflows/meningotype/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2210210917992673f792050a55c95b2e" ] ], - "timestamp": "2026-07-29T01:32:06.321275068", + "timestamp": "2026-07-30T00:36:08.262517224", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/merlindist/tests/main.nf.test.snap b/subworkflows/merlindist/tests/main.nf.test.snap index 931ebb963..d8ffc0c94 100644 --- a/subworkflows/merlindist/tests/main.nf.test.snap +++ b/subworkflows/merlindist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,a714676ea5e603813de6640079a3f847" ] ], - "timestamp": "2026-07-29T01:33:13.458420293", + "timestamp": "2026-07-30T00:37:21.789483284", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/midas/tests/main.nf.test.snap b/subworkflows/midas/tests/main.nf.test.snap index 4b6f778ba..1be7f32b5 100644 --- a/subworkflows/midas/tests/main.nf.test.snap +++ b/subworkflows/midas/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,66c2179f6d22e371b66b5d12ec5b0af1" ] ], - "timestamp": "2026-07-29T01:39:16.586672957", + "timestamp": "2026-07-30T00:43:18.74344166", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mlst/tests/main.nf.test.snap b/subworkflows/mlst/tests/main.nf.test.snap index e6e24d063..fb32b97c3 100644 --- a/subworkflows/mlst/tests/main.nf.test.snap +++ b/subworkflows/mlst/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-07-29T01:32:16.372288157", + "timestamp": "2026-07-30T00:36:55.791299455", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mobsuite/tests/main.nf.test.snap b/subworkflows/mobsuite/tests/main.nf.test.snap index 30119da3f..f83424fb0 100644 --- a/subworkflows/mobsuite/tests/main.nf.test.snap +++ b/subworkflows/mobsuite/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,e586a98fe29a48792ce661d2649ada18" ] ], - "timestamp": "2026-07-29T01:33:33.310297379", + "timestamp": "2026-07-30T00:38:13.125714476", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mykrobe/tests/main.nf.test.snap b/subworkflows/mykrobe/tests/main.nf.test.snap index 707dae741..42e6fefa0 100644 --- a/subworkflows/mykrobe/tests/main.nf.test.snap +++ b/subworkflows/mykrobe/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-29T01:32:26.08276497", + "timestamp": "2026-07-30T00:37:05.95887141", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ngmaster/tests/main.nf.test.snap b/subworkflows/ngmaster/tests/main.nf.test.snap index 410a35a14..b090900c9 100644 --- a/subworkflows/ngmaster/tests/main.nf.test.snap +++ b/subworkflows/ngmaster/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9dbc0e8b7902e955ec10c94c11074f06" ] ], - "timestamp": "2026-07-29T01:32:34.402363664", + "timestamp": "2026-07-30T00:37:09.347207654", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/nohuman/tests/main.nf.test.snap b/subworkflows/nohuman/tests/main.nf.test.snap index 594da4bc9..62c19208b 100644 --- a/subworkflows/nohuman/tests/main.nf.test.snap +++ b/subworkflows/nohuman/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,75d067d7ecc44ec6c90a321b8103c997" ] ], - "timestamp": "2026-07-29T01:37:10.520038223", + "timestamp": "2026-07-30T00:41:41.432319795", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/panaroo/tests/main.nf.test.snap b/subworkflows/panaroo/tests/main.nf.test.snap index b7927fe59..322357c5f 100644 --- a/subworkflows/panaroo/tests/main.nf.test.snap +++ b/subworkflows/panaroo/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,0e38cb68a88a1a2911e751e9a8ffd648" ] ], - "timestamp": "2026-07-29T01:34:04.286068861", + "timestamp": "2026-07-30T00:38:41.892273206", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pangenome/tests/main.nf.test.snap b/subworkflows/pangenome/tests/main.nf.test.snap index 4e0505db0..689ed8366 100644 --- a/subworkflows/pangenome/tests/main.nf.test.snap +++ b/subworkflows/pangenome/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:34:06.316490703", + "timestamp": "2026-07-30T00:38:43.444283472", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pasty/tests/main.nf.test.snap b/subworkflows/pasty/tests/main.nf.test.snap index a28502840..3089a75cc 100644 --- a/subworkflows/pasty/tests/main.nf.test.snap +++ b/subworkflows/pasty/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "versions.yml:md5,d806f451289eb221f11075799712603e" ] ], - "timestamp": "2026-07-29T21:47:10.992709384", + "timestamp": "2026-07-30T00:37:14.000856853", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pbptyper/tests/main.nf.test.snap b/subworkflows/pbptyper/tests/main.nf.test.snap index 2b55de6d5..d1a17282e 100644 --- a/subworkflows/pbptyper/tests/main.nf.test.snap +++ b/subworkflows/pbptyper/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18" ] ], - "timestamp": "2026-07-29T21:59:07.128112627", + "timestamp": "2026-07-30T00:37:57.287439735", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/phispy/tests/main.nf.test.snap b/subworkflows/phispy/tests/main.nf.test.snap index ae79b6c6b..504cea567 100644 --- a/subworkflows/phispy/tests/main.nf.test.snap +++ b/subworkflows/phispy/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-29T01:34:50.379277628", + "timestamp": "2026-07-30T00:40:16.532246227", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pirate/tests/main.nf.test.snap b/subworkflows/pirate/tests/main.nf.test.snap index 2ef88c474..4e0ab3f47 100644 --- a/subworkflows/pirate/tests/main.nf.test.snap +++ b/subworkflows/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,424257d69beae21355dee29eac16ca77" ] ], - "timestamp": "2026-07-29T01:35:28.739823018", + "timestamp": "2026-07-30T00:40:47.427737664", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/plasmidfinder/tests/main.nf.test.snap b/subworkflows/plasmidfinder/tests/main.nf.test.snap index 2be0d92fa..416162060 100644 --- a/subworkflows/plasmidfinder/tests/main.nf.test.snap +++ b/subworkflows/plasmidfinder/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-29T01:32:44.330042395", + "timestamp": "2026-07-30T00:38:15.852444954", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pneumocat/tests/main.nf.test.snap b/subworkflows/pneumocat/tests/main.nf.test.snap index ae6ad4cc2..7c76ef31f 100644 --- a/subworkflows/pneumocat/tests/main.nf.test.snap +++ b/subworkflows/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-29T01:33:05.586353018", + "timestamp": "2026-07-30T00:38:39.180792292", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/prokka/tests/main.nf.test.snap b/subworkflows/prokka/tests/main.nf.test.snap index d8a5b0926..1bf2bbcf0 100644 --- a/subworkflows/prokka/tests/main.nf.test.snap +++ b/subworkflows/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-29T01:32:59.993393914", + "timestamp": "2026-07-30T00:38:38.122207605", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/quast/tests/main.nf.test.snap b/subworkflows/quast/tests/main.nf.test.snap index 165d66eae..64539fb17 100644 --- a/subworkflows/quast/tests/main.nf.test.snap +++ b/subworkflows/quast/tests/main.nf.test.snap @@ -10,9 +10,6 @@ "scope": "sample" }, "SRR2838702.tsv:md5,a02f798379d9982810a198ec9b389079", - [ - "versions.yml:md5,83128d552544124c01b8b5502f773fc6" - ], { "id": "quast-QUAST:CSVTK_CONCAT", "logs_dir": "merged-results/logs/quast-concat/", @@ -25,7 +22,7 @@ "versions.yml:md5,f6625779099decc901ee6311371b1230" ] ], - "timestamp": "2026-07-29T01:32:58.257588548", + "timestamp": "2026-07-30T00:38:58.645483063", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/rgi/tests/main.nf.test.snap b/subworkflows/rgi/tests/main.nf.test.snap index 1a69fe461..2c0bf004d 100644 --- a/subworkflows/rgi/tests/main.nf.test.snap +++ b/subworkflows/rgi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,c1294552ba205b057bd368875a4eac93" ] ], - "timestamp": "2026-07-29T01:33:57.888308447", + "timestamp": "2026-07-30T00:40:03.980615536", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/roary/tests/main.nf.test.snap b/subworkflows/roary/tests/main.nf.test.snap index 76fa02697..2110ba8f1 100644 --- a/subworkflows/roary/tests/main.nf.test.snap +++ b/subworkflows/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d5496a62b5ffe9e5af444bfc53221551" ] ], - "timestamp": "2026-07-29T01:34:16.073320749", + "timestamp": "2026-07-30T00:40:19.847026733", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sccmec/tests/main.nf.test.snap b/subworkflows/sccmec/tests/main.nf.test.snap index 05b727022..440b95606 100644 --- a/subworkflows/sccmec/tests/main.nf.test.snap +++ b/subworkflows/sccmec/tests/main.nf.test.snap @@ -23,7 +23,7 @@ "versions.yml:md5,c6ede7b0533855a33c127cafa29de747" ] ], - "timestamp": "2026-07-29T21:36:47.21301389", + "timestamp": "2026-07-30T00:39:10.813370359", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scoary/tests/main.nf.test.snap b/subworkflows/scoary/tests/main.nf.test.snap index f3ffb8eb5..5bc53a554 100644 --- a/subworkflows/scoary/tests/main.nf.test.snap +++ b/subworkflows/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,36d9b366d4941f258a248bf7a31aecc7" ] ], - "timestamp": "2026-07-29T01:33:07.73530746", + "timestamp": "2026-07-30T00:39:07.465628311", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scrubber/tests/main.nf.test.snap b/subworkflows/scrubber/tests/main.nf.test.snap index 87045ab49..bff4edfea 100644 --- a/subworkflows/scrubber/tests/main.nf.test.snap +++ b/subworkflows/scrubber/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-29T01:37:56.542651421", + "timestamp": "2026-07-30T00:43:27.033020962", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-29T01:38:37.859104087", + "timestamp": "2026-07-30T00:44:00.513288867", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seqsero2/tests/main.nf.test.snap b/subworkflows/seqsero2/tests/main.nf.test.snap index 9854e178f..8e72353bb 100644 --- a/subworkflows/seqsero2/tests/main.nf.test.snap +++ b/subworkflows/seqsero2/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-29T01:33:12.95288607", + "timestamp": "2026-07-30T00:39:14.222160389", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seroba/tests/main.nf.test.snap b/subworkflows/seroba/tests/main.nf.test.snap index 48f827599..a7e130ecd 100644 --- a/subworkflows/seroba/tests/main.nf.test.snap +++ b/subworkflows/seroba/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,4fd4f724e2f19016eff39a2b524a9007" ] ], - "timestamp": "2026-07-29T01:34:08.925148331", + "timestamp": "2026-07-30T00:40:08.848418362", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigapass/tests/main.nf.test.snap b/subworkflows/shigapass/tests/main.nf.test.snap index e843f3c24..4528645ba 100644 --- a/subworkflows/shigapass/tests/main.nf.test.snap +++ b/subworkflows/shigapass/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f481607e2b7526fd798b2375bb3cc9c4" ] ], - "timestamp": "2026-07-29T01:33:30.972097787", + "timestamp": "2026-07-30T00:39:36.318062243", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigatyper/tests/main.nf.test.snap b/subworkflows/shigatyper/tests/main.nf.test.snap index cff538246..36b612788 100644 --- a/subworkflows/shigatyper/tests/main.nf.test.snap +++ b/subworkflows/shigatyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-07-29T01:33:27.637875945", + "timestamp": "2026-07-30T00:39:30.71064618", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigeifinder/tests/main.nf.test.snap b/subworkflows/shigeifinder/tests/main.nf.test.snap index 19d20e888..dd16e40dd 100644 --- a/subworkflows/shigeifinder/tests/main.nf.test.snap +++ b/subworkflows/shigeifinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,bb067649d1cb0b7cc78ced0baa36bf0e" ] ], - "timestamp": "2026-07-29T01:33:25.72757409", + "timestamp": "2026-07-30T00:39:37.775646804", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sistr/tests/main.nf.test.snap b/subworkflows/sistr/tests/main.nf.test.snap index 8aeab78a7..80e7030c1 100644 --- a/subworkflows/sistr/tests/main.nf.test.snap +++ b/subworkflows/sistr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-29T21:42:15.395460849", + "timestamp": "2026-07-30T00:40:14.391016151", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/core/tests/main.nf.test.snap b/subworkflows/snippy/core/tests/main.nf.test.snap index b24bf7a44..388a99584 100644 --- a/subworkflows/snippy/core/tests/main.nf.test.snap +++ b/subworkflows/snippy/core/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-29T11:32:49.156063798", + "timestamp": "2026-07-30T00:40:23.733781279", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/run/tests/main.nf.test.snap b/subworkflows/snippy/run/tests/main.nf.test.snap index 717e1231d..015629a14 100644 --- a/subworkflows/snippy/run/tests/main.nf.test.snap +++ b/subworkflows/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30" ] ], - "timestamp": "2026-07-29T11:33:05.322847047", + "timestamp": "2026-07-30T00:40:55.55304233", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snpdists/tests/main.nf.test.snap b/subworkflows/snpdists/tests/main.nf.test.snap index 5d24bb230..a670303c6 100644 --- a/subworkflows/snpdists/tests/main.nf.test.snap +++ b/subworkflows/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b7c9ec6305cc1637c144c82ba20a94d6" ] ], - "timestamp": "2026-07-29T01:33:43.230896597", + "timestamp": "2026-07-30T00:40:48.890416169", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/spatyper/tests/main.nf.test.snap b/subworkflows/spatyper/tests/main.nf.test.snap index 5cfad3c31..ab2a69d7c 100644 --- a/subworkflows/spatyper/tests/main.nf.test.snap +++ b/subworkflows/spatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2be001b7db8743258dd915dfe57337f4" ] ], - "timestamp": "2026-07-29T01:33:53.98024966", + "timestamp": "2026-07-30T00:40:59.792203588", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/srahumanscrubber/tests/main.nf.test.snap b/subworkflows/srahumanscrubber/tests/main.nf.test.snap index d675017d7..e40c5ac65 100644 --- a/subworkflows/srahumanscrubber/tests/main.nf.test.snap +++ b/subworkflows/srahumanscrubber/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,ca8ec5702526f2d59b7e3c5068c1c400" ] ], - "timestamp": "2026-07-29T01:35:36.408683648", + "timestamp": "2026-07-30T00:42:49.312195453", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ssuissero/tests/main.nf.test.snap b/subworkflows/ssuissero/tests/main.nf.test.snap index 1b423b1d8..00fde3976 100644 --- a/subworkflows/ssuissero/tests/main.nf.test.snap +++ b/subworkflows/ssuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b273046b082dd70970b8f4e189aa5498" ] ], - "timestamp": "2026-07-29T01:33:48.816895407", + "timestamp": "2026-07-30T00:41:09.156836132", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphopiasccmec/tests/main.nf.test.snap b/subworkflows/staphopiasccmec/tests/main.nf.test.snap index c0d457518..925fc21ac 100644 --- a/subworkflows/staphopiasccmec/tests/main.nf.test.snap +++ b/subworkflows/staphopiasccmec/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f59d6534316ffe1998c60f98b212d80f" ] ], - "timestamp": "2026-07-29T01:33:55.304626746", + "timestamp": "2026-07-30T00:41:15.267714089", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphscan/tests/main.nf.test.snap b/subworkflows/staphscan/tests/main.nf.test.snap index 1eeaf8f89..006ce5699 100644 --- a/subworkflows/staphscan/tests/main.nf.test.snap +++ b/subworkflows/staphscan/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b" ] ], - "timestamp": "2026-07-29T01:34:07.256604501", + "timestamp": "2026-07-30T00:41:32.589847961", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stecfinder/tests/main.nf.test.snap b/subworkflows/stecfinder/tests/main.nf.test.snap index e754d2f50..893d5e3d7 100644 --- a/subworkflows/stecfinder/tests/main.nf.test.snap +++ b/subworkflows/stecfinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,a4e0bfe59670d712011a3dc00f3abeb5" ] ], - "timestamp": "2026-07-29T01:33:56.00198215", + "timestamp": "2026-07-30T00:41:23.126852804", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stxtyper/tests/main.nf.test.snap b/subworkflows/stxtyper/tests/main.nf.test.snap index a069132eb..9a51b7ecf 100644 --- a/subworkflows/stxtyper/tests/main.nf.test.snap +++ b/subworkflows/stxtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c" ] ], - "timestamp": "2026-07-29T01:33:57.762548904", + "timestamp": "2026-07-30T00:41:29.62237883", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sylph/tests/main.nf.test.snap b/subworkflows/sylph/tests/main.nf.test.snap index 209dd116d..244474c21 100644 --- a/subworkflows/sylph/tests/main.nf.test.snap +++ b/subworkflows/sylph/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2a85d1cd25d2a88c77d90030e05e17cf" ] ], - "timestamp": "2026-07-29T01:35:05.468492084", + "timestamp": "2026-07-30T00:42:36.144854671", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastn/tests/main.nf.test.snap b/subworkflows/tblastn/tests/main.nf.test.snap index 5d78b6da9..05644a628 100644 --- a/subworkflows/tblastn/tests/main.nf.test.snap +++ b/subworkflows/tblastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,413650f494aaf14a524501ce6dc5c959" ] ], - "timestamp": "2026-07-29T01:34:01.813740555", + "timestamp": "2026-07-30T00:41:29.658176168", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastx/tests/main.nf.test.snap b/subworkflows/tblastx/tests/main.nf.test.snap index 74f300929..7c2b5e271 100644 --- a/subworkflows/tblastx/tests/main.nf.test.snap +++ b/subworkflows/tblastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ 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"SRR2838702_R1.scrubbed.fastq.gz,SRR2838702_R2.scrubbed.fastq.gz" - }, - [ - "versions.yml:md5,7d27773f1e349726172140b0c615a73b" - ] + } ], - "timestamp": "2026-07-29T01:42:33.525627479", + "timestamp": "2026-07-30T00:49:55.974959825", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/traitar/tests/main.nf.test.snap b/subworkflows/traitar/tests/main.nf.test.snap index f39d0e955..e74f39b92 100644 --- a/subworkflows/traitar/tests/main.nf.test.snap +++ b/subworkflows/traitar/tests/main.nf.test.snap @@ -35,7 +35,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-29T01:40:06.183091617", + "timestamp": "2026-07-30T00:47:50.554103931", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 42d0c0f53..5e3c5bba7 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -165,20 +165,10 @@ "bactopia-runs/bactopia/nf-reports/bactopia-timeline.html" ], [ - 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a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-29T01:35:38.998880103", + "timestamp": "2026-07-30T00:44:04.175633039", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap index ea2db0fb2..9889cf922 100644 --- a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap @@ -26,10 +26,10 @@ "bactopia-runs/eggnog/nf-reports/eggnog-timeline.html" ], [ - "versions.yml:md5,56dfcc706d4c6949d6ff76e4274da031" + ] ], - "timestamp": "2026-07-29T01:40:37.864411574", + "timestamp": "2026-07-30T00:49:56.471588516", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap index 5a88de87f..f4fe544d0 100644 --- a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-29T01:35:26.657973043", + "timestamp": "2026-07-30T00:44:21.091331159", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-29T01:35:57.257668202", + "timestamp": "2026-07-30T00:44:49.719035522", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap index 83dd2ba43..cc8d43964 100644 --- a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap @@ -38,7 +38,7 @@ 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b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-29T01:36:03.090230544", + "timestamp": "2026-07-30T00:45:29.195653485", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap index 956ba75ec..68e023005 100644 --- a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap @@ -47,7 +47,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-29T01:40:19.298577757", + "timestamp": "2026-07-30T00:50:01.444745006", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap index 634fd48ec..c7bce652b 100644 --- a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap @@ -61,7 +61,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-29T01:36:16.965061126", + "timestamp": "2026-07-30T00:45:50.612267949", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap index 881c87a87..5822d1593 100644 --- a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-29T01:36:06.775856956", + "timestamp": "2026-07-30T00:45:45.528481711", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap index 2467ec2ae..54d081595 100644 --- a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap @@ -1068,7 +1068,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-29T01:36:56.157718753", + "timestamp": "2026-07-30T00:47:37.732911537", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap index fe6a2f397..a7c77b633 100644 --- a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-29T01:37:00.813038011", + "timestamp": "2026-07-30T00:47:30.390911941", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap index b621ba5d2..8814fff7c 100644 --- a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-29T01:41:29.129678843", + "timestamp": "2026-07-30T00:52:55.969610984", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -63,7 +63,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-29T01:41:59.441065364", + "timestamp": "2026-07-30T00:53:44.4624829", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap index d0c26cd62..43b666c63 100644 --- a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-29T01:36:39.097407223", + "timestamp": "2026-07-30T00:47:37.823359316", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap index df1e4240e..b3b368c57 100644 --- a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-29T01:36:38.262569677", + "timestamp": "2026-07-30T00:47:44.621782457", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap index 525105f43..057e738ec 100644 --- a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap @@ -43,7 +43,7 @@ "mashdist.tsv:md5,630500729ddf987a8f487cd409d0afce" ] ], - "timestamp": "2026-07-29T01:36:42.094510609", + "timestamp": "2026-07-30T00:47:55.734051336", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap index c7ef3c62e..1711f75c1 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "mashtree.dnd:md5,2b2d08b0bf16e25717f5db0eca6eba6b" ] ], - "timestamp": "2026-07-29T01:36:43.913834134", + "timestamp": "2026-07-30T00:47:56.939857226", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "mashtree.dnd:md5,02f89fd1a5f4a3a92df0b016061f67dd" ] ], - "timestamp": "2026-07-29T01:37:13.049369818", + "timestamp": "2026-07-30T00:48:27.071126803", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap index 09e55cd95..3c49f2ca8 100644 --- a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "mcroni.tsv:md5,c5459d2965dfafe22f173023d0c35610" ] ], - "timestamp": "2026-07-29T01:36:49.896482144", + "timestamp": "2026-07-30T00:48:02.987215097", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap index 8e68ebcd8..f4e8e7874 100644 --- a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "meningotype.tsv:md5,cdf1cbd9f28a9ce2138f072c6d0ab391" ] ], - "timestamp": "2026-07-29T01:36:49.846022063", + "timestamp": "2026-07-30T00:48:06.017330495", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap index 7934782c7..4ea1cc3e4 100644 --- a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap @@ -386,7 +386,7 @@ ] ], - "timestamp": "2026-07-29T01:38:36.700683413", + "timestamp": "2026-07-30T00:49:36.893153419", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -973,7 +973,7 @@ ] ], - "timestamp": "2026-07-29T01:40:27.32965059", + "timestamp": "2026-07-30T00:51:53.879010331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/midas/tests/main.nf.test.snap b/workflows/bactopia-tools/midas/tests/main.nf.test.snap index c56951f3f..d789382f1 100644 --- a/workflows/bactopia-tools/midas/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/midas/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-29T01:37:29.568331075", + "timestamp": "2026-07-30T00:48:41.343249956", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -99,7 +99,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-29T01:38:33.559499623", + "timestamp": "2026-07-30T00:49:23.034024271", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap index a2efc40b7..4d8864f1f 100644 --- a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "mlst.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6" ] ], - "timestamp": "2026-07-29T01:36:57.602958653", + "timestamp": "2026-07-30T00:48:15.899678948", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap index 41d0d8e05..81bcc9b32 100644 --- a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "mobsuite.tsv:md5,951dbd706ab78c4d00aa28735ab34e87" ] ], - "timestamp": "2026-07-29T01:37:39.525998546", + "timestamp": "2026-07-30T00:48:44.483859763", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap index 9e1f75e25..b8de1a178 100644 --- a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap @@ -41,7 +41,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-29T01:37:03.270460416", + "timestamp": "2026-07-30T00:48:20.875202495", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap index 64598556c..dece7a5f8 100644 --- a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ngmaster.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219" ] ], - "timestamp": "2026-07-29T01:37:09.555667277", + "timestamp": "2026-07-30T00:48:35.79817481", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap index 469dec85b..1c2f55ab7 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap @@ -140,7 +140,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:44:38.676764579", + "timestamp": "2026-07-30T00:57:18.524040932", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -314,7 +314,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:42:19.838411501", + "timestamp": "2026-07-30T00:54:30.123243986", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -447,7 +447,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:43:31.086283461", + "timestamp": "2026-07-30T00:56:01.463760918", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -579,7 +579,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:38:38.008748726", + "timestamp": "2026-07-30T00:49:59.982072905", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -663,7 +663,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:39:42.265173667", + "timestamp": "2026-07-30T00:51:11.913708352", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -747,7 +747,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-29T01:40:54.197027582", + "timestamp": "2026-07-30T00:52:45.306300316", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap index 07f83b486..a80784b69 100644 --- a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap @@ -41,7 +41,7 @@ ] ], - "timestamp": "2026-07-29T21:47:17.211995656", + "timestamp": "2026-07-30T00:48:43.962318083", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap index ad190aa3a..d6b220719 100644 --- a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap @@ -40,7 +40,7 @@ ] ], - "timestamp": "2026-07-29T21:59:12.623312651", + "timestamp": "2026-07-30T00:49:33.255684955", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap index e99d2b607..f852c32fd 100644 --- a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap @@ -60,7 +60,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-29T01:38:16.712434613", + "timestamp": "2026-07-30T00:49:56.554959703", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap index 5933c5fdc..39d294aee 100644 --- a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-29T01:37:25.026660028", + "timestamp": "2026-07-30T00:49:16.446450824", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap index 4d820228b..22471381e 100644 --- a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-29T01:37:25.257893434", + "timestamp": "2026-07-30T00:49:13.046931953", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap index 8902df7e4..759bdc8e4 100644 --- a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-29T01:37:39.540498378", + "timestamp": "2026-07-30T00:49:19.08682362", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/quast/tests/main.nf.test.snap b/workflows/bactopia-tools/quast/tests/main.nf.test.snap index 2a0f3540e..343920b14 100644 --- a/workflows/bactopia-tools/quast/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/quast/tests/main.nf.test.snap @@ -58,18 +58,16 @@ ], [ "SRR2838702.tsv:md5,a02f798379d9982810a198ec9b389079", - "versions.yml:md5,83128d552544124c01b8b5502f773fc6", "SRR2838702_glimmer_genes.gff:md5,36b7926c51f078321f2fd6867a4de85a", "report.tex:md5,04c0dc621c59c716c7c99a57c6eba3c6", "report.tsv:md5,8c0257e77c7bb49f734e68054cb3fcdc", "report.txt:md5,d35e1ed08c41cc6e391297a2885ed278", "transposed_report.tex:md5,92a642be48f2ed8e9d45f32aed4713a2", "transposed_report.txt:md5,652a64d08ecdfe0b26fd918815575737", - "versions.yml:md5,f6625779099decc901ee6311371b1230", "quast.tsv:md5,a02f798379d9982810a198ec9b389079" ] ], - "timestamp": "2026-07-29T01:37:40.847741354", + "timestamp": "2026-07-30T00:49:29.718406164", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap index 53a4b0693..baac6972c 100644 --- a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap @@ -76,7 +76,7 @@ "versions.yml:md5,69941ec700f55e09c1a930ed36f54b0c" ] ], - "timestamp": "2026-07-29T01:38:37.072072086", + "timestamp": "2026-07-30T00:50:15.440279652", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap index 8cf4b46ce..1f35e7dd1 100644 --- a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap @@ -43,7 +43,7 @@ ] ], - "timestamp": "2026-07-29T21:37:10.373092259", + "timestamp": "2026-07-30T00:50:28.566688238", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -93,7 +93,7 @@ ] ], - "timestamp": "2026-07-29T21:36:53.434687545", + "timestamp": "2026-07-30T00:50:01.429639754", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap index 69d5edbbd..74f530e63 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "scrubber.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d" ] ], - "timestamp": "2026-07-29T01:37:56.966328894", + "timestamp": "2026-07-30T00:50:21.45880484", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -96,7 +96,7 @@ "scrubber.tsv:md5,e957775ff85716621f5fdd536de5b417" ] ], - "timestamp": "2026-07-29T01:42:14.657285073", + "timestamp": "2026-07-30T00:53:28.98919548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "scrubber.tsv:md5,9554a4a6929bbfd485e28acd4a716772" ] ], - "timestamp": "2026-07-29T01:43:05.742795155", + "timestamp": "2026-07-30T00:54:37.238847702", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap index bed78f482..baed5d133 100644 --- a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-29T01:37:40.798731672", + "timestamp": "2026-07-30T00:50:05.226773952", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap index e33ff9a08..c04da941e 100644 --- a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "seroba.tsv:md5,8c20690cc5ca0fd77228c830001e0b86" ] ], - "timestamp": "2026-07-29T01:38:21.84953609", + "timestamp": "2026-07-30T00:50:40.633000005", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap index edb8ea411..02a76f0cd 100644 --- a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "shigapass.tsv:md5,9982dbc252423a0507b7c397f66164f2" ] ], - "timestamp": "2026-07-29T01:37:50.673257637", + "timestamp": "2026-07-30T00:50:27.038048511", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap index fbe9db514..078cacf59 100644 --- a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap @@ -74,11 +74,10 @@ "SRR13039589-hits.tsv:md5,7bdab5d495d8424b2df3005773ef1364", "SRR13039589.tsv:md5,8ab32470875fe923b8d338da4ca35d1c", "versions.yml:md5,ae04a8f8ba5f8b41af9b6af75fecfd17", - "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e", - "shigatyper.tsv:md5,6041948e454daeabef20a6f725047dca" + "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-07-29T01:37:46.020804099", + "timestamp": "2026-07-30T00:50:33.174366621", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap index 6027dab5a..f01a4005c 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b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "stxtyper.tsv:md5,99f9ffe60fe519d684ee7943641022d2" ] ], - "timestamp": "2026-07-29T01:38:35.338512059", + "timestamp": "2026-07-30T00:51:38.769202833", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap index 0d68c8c8c..5d0f09b84 100644 --- a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "sylph.tsv:md5,beb99cbcea3c9c0a90329ae09ee957f3" ] ], - "timestamp": "2026-07-29T01:39:20.727418276", + "timestamp": "2026-07-30T00:52:24.032040616", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap index 8fc3da1d3..549dacf98 100644 --- a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-29T01:38:35.493868294", + "timestamp": "2026-07-30T00:51:35.302322173", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-29T01:38:58.6249142", + "timestamp": "2026-07-30T00:51:57.439961888", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap index 942098087..0dd6cdbe7 100644 --- a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-29T01:38:37.053076265", + "timestamp": "2026-07-30T00:51:36.274913894", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-29T01:39:22.712807122", + "timestamp": "2026-07-30T00:52:19.45682325", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "tblastx.tsv:md5,4efa1d2d8633246603e06df64e559c4c" ] ], - "timestamp": "2026-07-29T01:39:03.537385195", + "timestamp": "2026-07-30T00:51:56.001229892", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap index dbabcf818..86bc826c4 100644 --- a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-07-29T01:39:09.110218015", + "timestamp": "2026-07-30T00:52:30.057210326", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap index 0f1572bba..2a1b03913 100644 --- a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-29T01:42:43.280691904", + "timestamp": "2026-07-30T00:56:35.787166831", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/cleanyerreads/tests/main.nf.test.snap b/workflows/cleanyerreads/tests/main.nf.test.snap index dbc933968..8ba4b8bbf 100644 --- a/workflows/cleanyerreads/tests/main.nf.test.snap +++ b/workflows/cleanyerreads/tests/main.nf.test.snap @@ -80,14 +80,10 @@ "bactopia-runs/cleanyerreads/nf-reports/cleanyerreads-timeline.html" ], [ - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", - "versions.yml:md5,74fd99ec158fe3e666d2ba871c809827", - "versions.yml:md5,61924107a406c136f55c445d470721f7", - "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" + ] ], - "timestamp": "2026-07-29T01:40:58.602321074", + "timestamp": "2026-07-30T00:54:46.650311486", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -158,12 +154,10 @@ "bactopia-runs/cleanyerreads/nf-reports/cleanyerreads-timeline.html" ], [ - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", - "versions.yml:md5,61924107a406c136f55c445d470721f7" + ] ], - "timestamp": "2026-07-29T01:39:40.987158505", + "timestamp": "2026-07-30T00:53:26.016521297", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/staphopia/tests/main.nf.test.snap b/workflows/staphopia/tests/main.nf.test.snap index 171aea251..8a07bde28 100644 --- a/workflows/staphopia/tests/main.nf.test.snap +++ b/workflows/staphopia/tests/main.nf.test.snap @@ -268,28 +268,10 @@ "bactopia-runs/staphopia/nf-reports/staphopia-timeline.html" ], [ - "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e", - "versions.yml:md5,5d00225a5ad24de728e651fdd0d7d1e3", - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,d86b6a7bb7117ed6a86a0bd9f45e0377", - "versions.yml:md5,e46de3078794860a978e2dd0b390c27c", - "versions.yml:md5,c0b16a8b5ea1a55c72f38545beffb659", - "versions.yml:md5,9ca3ec85a3c0993ed41a25321fd6d423", - "versions.yml:md5,55b934f1c8a9ffdd523a01a6e4d87a5e", - "versions.yml:md5,4d90b86147c4eb115fc93edc4fa484b8", - "versions.yml:md5,32d57feabda90e9fe6e0aeb96e5d2352", - "versions.yml:md5,70a740425288fd57db5b227c8a1b3723", - "versions.yml:md5,d203f21af354f31f3d144e58af47cff3", - "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6", - "versions.yml:md5,1913efda4329af168df4ab88555dbeb4", - "versions.yml:md5,61924107a406c136f55c445d470721f7", - "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc", - "versions.yml:md5,35f4a9f839e9fd13b2afb63fecea88b4", - "versions.yml:md5,db2a4ba0c195fd025b9a8068ad991793", - "versions.yml:md5,c707d4291d068c2b150937480568d0b0" + ] ], - "timestamp": "2026-07-29T01:43:09.961549011", + "timestamp": "2026-07-30T00:57:24.825957304", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/teton/tests/main.nf.test.snap b/workflows/teton/tests/main.nf.test.snap index 31efd2667..84bbea363 100644 --- a/workflows/teton/tests/main.nf.test.snap +++ b/workflows/teton/tests/main.nf.test.snap @@ -166,22 +166,10 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", - "versions.yml:md5,7d27773f1e349726172140b0c615a73b", - "versions.yml:md5,b567c9f0928098cfc68f12308a3372f0", - "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", - "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", - "versions.yml:md5,61924107a406c136f55c445d470721f7", - "versions.yml:md5,b529c3993efa987da9a980fe7c8061f8", - "versions.yml:md5,7365b17a2c11eb3d256b0facd20a197a", - "versions.yml:md5,340e424aa721674cf14433027027114a", - "versions.yml:md5,f27b3200ffeb3e669ad225b87cedf06c", - "versions.yml:md5,fcfb282f67fc93a18b7d921d22e70628", - "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" + ] ], - "timestamp": "2026-07-29T01:42:35.103899724", + "timestamp": "2026-07-30T00:57:47.488165977", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -353,22 +341,10 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", - "versions.yml:md5,7d27773f1e349726172140b0c615a73b", - "versions.yml:md5,5ccb1a29e9b0dfff5b4a46a6e73facf3", - "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", - "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", - "versions.yml:md5,61924107a406c136f55c445d470721f7", - "versions.yml:md5,b529c3993efa987da9a980fe7c8061f8", - "versions.yml:md5,7365b17a2c11eb3d256b0facd20a197a", - "versions.yml:md5,340e424aa721674cf14433027027114a", - "versions.yml:md5,f27b3200ffeb3e669ad225b87cedf06c", - "versions.yml:md5,fcfb282f67fc93a18b7d921d22e70628", - "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" + ] ], - "timestamp": "2026-07-29T01:52:19.727815772", + "timestamp": "2026-07-30T01:10:34.945146971", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -540,22 +516,10 @@ "merged-results/logs/SRR2838702-join/versions.yml" ], [ - "versions.yml:md5,d3dfbd01b2627f6ea7b5fd201512c39d", - "versions.yml:md5,6244b9a467c68aa03fd62d84f370f31a", - "versions.yml:md5,7d27773f1e349726172140b0c615a73b", - "versions.yml:md5,14feb3b47ba66dc6b247bdd7debcc18c", - "versions.yml:md5,044131149bd3aa2556576fb17c9925a3", - "versions.yml:md5,1e53d17af5b9008b9442ff5d18670fbe", - "versions.yml:md5,61924107a406c136f55c445d470721f7", - "versions.yml:md5,b529c3993efa987da9a980fe7c8061f8", - "versions.yml:md5,7365b17a2c11eb3d256b0facd20a197a", - "versions.yml:md5,340e424aa721674cf14433027027114a", - "versions.yml:md5,f27b3200ffeb3e669ad225b87cedf06c", - "versions.yml:md5,fcfb282f67fc93a18b7d921d22e70628", - "versions.yml:md5,e99779aecd8dce47f4bef01bc23da898" + ] ], - "timestamp": "2026-07-29T01:47:11.054654393", + "timestamp": "2026-07-30T01:06:24.244779926", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 64a2b518e7b800340e28bbe2b8c36f013b2bf5d9 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 12:39:57 -0600 Subject: [PATCH 33/43] update snapshots bump plugin version --- .claude/docs/project/04-testing-framework.md | 2 +- .claude/skills/run-tests/SKILL.md | 2 +- CHANGELOG.md | 9 +++++++++ catalog.json | 4 ++-- conf/test_base.config | 2 +- data/conda/meta.yaml | 2 +- modules/abricate/run/tests/main.nf.test.snap | 2 +- .../abricate/summary/tests/main.nf.test.snap | 2 +- modules/abritamr/run/tests/main.nf.test.snap | 4 ++-- modules/agrvate/main.nf | 10 ++++------ modules/agrvate/tests/main.nf.test.snap | 4 ++-- .../amrfinderplus/run/tests/main.nf.test.snap | 4 ++-- modules/ariba/getref/module.config | 2 +- modules/ariba/run/module.config | 2 +- modules/ariba/run/tests/main.nf.test.snap | 2 +- .../bactopia/assembler/tests/main.nf.test.snap | 16 ++++++++-------- .../bactopia/gather/tests/main.nf.test.snap | 16 ++++++++-------- modules/bactopia/qc/tests/main.nf.test.snap | 10 +++++----- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- modules/bactopia/teton/tests/main.nf.test.snap | 4 ++-- modules/bakta/run/tests/main.nf.test.snap | 4 ++-- modules/blast/blastn/tests/main.nf.test.snap | 2 +- modules/blast/blastp/tests/main.nf.test.snap | 2 +- modules/blast/blastx/tests/main.nf.test.snap | 2 +- modules/blast/tblastn/tests/main.nf.test.snap | 2 +- modules/blast/tblastx/tests/main.nf.test.snap | 2 +- modules/bracken/tests/main.nf.test.snap | 4 ++-- modules/btyper3/tests/main.nf.test.snap | 4 ++-- modules/busco/tests/main.nf.test.snap | 4 ++-- .../checkm/lineagewf/tests/main.nf.test.snap | 4 ++-- .../checkm2/predict/tests/main.nf.test.snap | 4 ++-- modules/clermontyping/module.config | 2 +- modules/clermontyping/tests/main.nf.test.snap | 4 ++-- modules/clonalframeml/module.config | 2 +- modules/clonalframeml/tests/main.nf.test.snap | 4 ++-- modules/csvtk/concat/tests/main.nf.test.snap | 4 ++-- modules/csvtk/join/tests/main.nf.test.snap | 4 ++-- modules/deacon/filter/tests/main.nf.test.snap | 6 +++--- .../defensefinder/run/tests/main.nf.test.snap | 2 +- modules/ectyper/tests/main.nf.test.snap | 4 ++-- modules/eggnog/mapper/tests/main.nf.test.snap | 4 ++-- modules/emmtyper/tests/main.nf.test.snap | 6 +++--- modules/fastani/tests/main.nf.test.snap | 4 ++-- modules/gamma/main.nf | 10 ++++------ modules/gamma/tests/main.nf.test.snap | 4 ++-- modules/genomedl/tests/main.nf.test.snap | 6 +++--- modules/genotyphi/parse/module.config | 2 +- .../genotyphi/parse/tests/main.nf.test.snap | 2 +- modules/gigatyper/tests/main.nf.test.snap | 2 +- .../gtdbtk/classifywf/tests/main.nf.test.snap | 2 +- modules/gubbins/tests/main.nf.test.snap | 4 ++-- modules/hicap/module.config | 2 +- modules/hicap/tests/main.nf.test.snap | 8 ++++---- modules/hpsuissero/tests/main.nf.test.snap | 4 ++-- modules/iqtree/tests/main.nf.test.snap | 4 ++-- modules/ismapper/module.config | 2 +- modules/ismapper/tests/main.nf.test.snap | 2 +- modules/kleborate/tests/main.nf.test.snap | 2 +- modules/kraken2/tests/main.nf.test.snap | 4 ++-- modules/legsta/tests/main.nf.test.snap | 2 +- modules/lissero/tests/main.nf.test.snap | 4 ++-- modules/mash/dist/tests/main.nf.test.snap | 4 ++-- modules/mashtree/tests/main.nf.test.snap | 2 +- modules/mcroni/module.config | 2 +- modules/mcroni/tests/main.nf.test.snap | 4 ++-- modules/meningotype/tests/main.nf.test.snap | 4 ++-- modules/merlin/dist/tests/main.nf.test.snap | 4 ++-- modules/midas/species/tests/main.nf.test.snap | 4 ++-- modules/mlst/tests/main.nf.test.snap | 2 +- modules/mobsuite/recon/tests/main.nf.test.snap | 6 +++--- modules/mykrobe/predict/module.config | 2 +- modules/mykrobe/predict/tests/main.nf.test | 10 +++++++--- .../mykrobe/predict/tests/main.nf.test.snap | 4 +--- modules/ngmaster/tests/main.nf.test.snap | 4 ++-- modules/nohuman/run/tests/main.nf.test.snap | 6 +++--- modules/panaroo/run/tests/main.nf.test.snap | 2 +- modules/pasty/tests/main.nf.test.snap | 2 +- modules/pbptyper/tests/main.nf.test.snap | 2 +- modules/phispy/tests/main.nf.test.snap | 2 +- modules/pirate/tests/main.nf.test.snap | 2 +- modules/plasmidfinder/tests/main.nf.test.snap | 4 ++-- modules/pneumocat/tests/main.nf.test.snap | 2 +- modules/prokka/tests/main.nf.test.snap | 6 +++--- modules/quast/tests/main.nf.test.snap | 6 +++--- modules/rgi/heatmap/tests/main.nf.test.snap | 2 +- modules/rgi/main/tests/main.nf.test.snap | 6 +++--- modules/roary/tests/main.nf.test.snap | 2 +- modules/sccmec/tests/main.nf.test.snap | 4 ++-- modules/scoary/tests/main.nf.test.snap | 2 +- modules/seqsero2/tests/main.nf.test.snap | 4 ++-- modules/seroba/run/tests/main.nf.test.snap | 2 +- modules/shigapass/tests/main.nf.test.snap | 4 ++-- modules/shigatyper/tests/main.nf.test.snap | 2 +- modules/shigeifinder/module.config | 2 +- modules/shigeifinder/tests/main.nf.test.snap | 4 ++-- modules/sistr/module.config | 2 +- modules/sistr/tests/main.nf.test.snap | 4 ++-- modules/snippy/core/tests/main.nf.test.snap | 2 +- modules/snippy/run/module.config | 2 +- modules/snippy/run/tests/main.nf.test.snap | 4 ++-- modules/snpdists/tests/main.nf.test.snap | 2 +- modules/spatyper/tests/main.nf.test.snap | 4 ++-- .../scrub/tests/main.nf.test.snap | 4 ++-- modules/ssuissero/tests/main.nf.test.snap | 4 ++-- .../staphopiasccmec/tests/main.nf.test.snap | 4 ++-- modules/staphscan/tests/main.nf.test.snap | 2 +- modules/stecfinder/tests/main.nf.test.snap | 6 +++--- modules/stxtyper/tests/main.nf.test.snap | 2 +- modules/sylph/profile/tests/main.nf.test.snap | 4 ++-- .../tbprofiler/collate/tests/main.nf.test.snap | 2 +- .../tbprofiler/profile/tests/main.nf.test.snap | 6 +++--- modules/traitar/run/main.nf | 15 ++++++--------- modules/traitar/run/tests/main.nf.test.snap | 4 ++-- nextflow.config | 2 +- subworkflows/abricate/tests/main.nf.test.snap | 2 +- subworkflows/abritamr/tests/main.nf.test.snap | 2 +- subworkflows/agrvate/tests/main.nf.test.snap | 2 +- .../amrfinderplus/tests/main.nf.test.snap | 2 +- subworkflows/ariba/tests/main.nf.test.snap | 2 +- .../bactopia/sketcher/tests/main.nf.test.snap | 2 +- subworkflows/bakta/tests/main.nf.test.snap | 2 +- subworkflows/blastn/tests/main.nf.test.snap | 2 +- subworkflows/blastp/tests/main.nf.test.snap | 2 +- subworkflows/blastx/tests/main.nf.test.snap | 2 +- subworkflows/btyper3/tests/main.nf.test.snap | 2 +- subworkflows/busco/tests/main.nf.test.snap | 2 +- subworkflows/checkm/tests/main.nf.test.snap | 2 +- subworkflows/checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../clonalframeml/tests/main.nf.test.snap | 2 +- subworkflows/deacon/tests/main.nf.test.snap | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- subworkflows/ectyper/tests/main.nf.test.snap | 2 +- subworkflows/eggnog/tests/main.nf.test.snap | 2 +- subworkflows/emmtyper/tests/main.nf.test.snap | 2 +- subworkflows/fastani/tests/main.nf.test.snap | 2 +- subworkflows/gamma/tests/main.nf.test.snap | 2 +- subworkflows/genomedl/tests/main.nf.test.snap | 6 +++--- subworkflows/genotyphi/tests/main.nf.test.snap | 2 +- subworkflows/gigatyper/tests/main.nf.test.snap | 2 +- subworkflows/gtdb/tests/main.nf.test.snap | 2 +- subworkflows/gubbins/tests/main.nf.test.snap | 2 +- subworkflows/hicap/tests/main.nf.test.snap | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- subworkflows/iqtree/tests/main.nf.test.snap | 2 +- subworkflows/ismapper/tests/main.nf.test.snap | 2 +- subworkflows/kleborate/tests/main.nf.test.snap | 2 +- subworkflows/kraken2/tests/main.nf.test.snap | 2 +- subworkflows/legsta/tests/main.nf.test.snap | 2 +- subworkflows/lissero/tests/main.nf.test.snap | 2 +- subworkflows/mashdist/tests/main.nf.test.snap | 2 +- subworkflows/mashtree/tests/main.nf.test.snap | 2 +- subworkflows/mcroni/tests/main.nf.test.snap | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../merlindist/tests/main.nf.test.snap | 2 +- subworkflows/midas/tests/main.nf.test.snap | 2 +- subworkflows/mlst/tests/main.nf.test.snap | 2 +- subworkflows/mobsuite/tests/main.nf.test.snap | 2 +- subworkflows/mykrobe/tests/main.nf.test | 8 ++++++-- subworkflows/mykrobe/tests/main.nf.test.snap | 4 +--- subworkflows/ngmaster/tests/main.nf.test.snap | 2 +- subworkflows/nohuman/tests/main.nf.test.snap | 2 +- subworkflows/panaroo/tests/main.nf.test.snap | 2 +- subworkflows/pangenome/tests/main.nf.test.snap | 2 +- subworkflows/pasty/tests/main.nf.test.snap | 2 +- subworkflows/pbptyper/tests/main.nf.test.snap | 2 +- subworkflows/phispy/tests/main.nf.test.snap | 2 +- subworkflows/pirate/tests/main.nf.test.snap | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- subworkflows/pneumocat/tests/main.nf.test.snap | 2 +- subworkflows/prokka/tests/main.nf.test.snap | 2 +- subworkflows/quast/tests/main.nf.test.snap | 2 +- subworkflows/rgi/tests/main.nf.test.snap | 2 +- subworkflows/roary/tests/main.nf.test.snap | 2 +- subworkflows/sccmec/tests/main.nf.test.snap | 2 +- subworkflows/scoary/tests/main.nf.test.snap | 2 +- subworkflows/scrubber/tests/main.nf.test.snap | 4 ++-- subworkflows/seqsero2/tests/main.nf.test.snap | 2 +- subworkflows/seroba/tests/main.nf.test.snap | 2 +- subworkflows/shigapass/tests/main.nf.test.snap | 2 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- subworkflows/sistr/tests/main.nf.test.snap | 2 +- .../snippy/core/tests/main.nf.test.snap | 2 +- .../snippy/run/tests/main.nf.test.snap | 2 +- subworkflows/snpdists/tests/main.nf.test.snap | 2 +- subworkflows/spatyper/tests/main.nf.test.snap | 2 +- .../srahumanscrubber/tests/main.nf.test.snap | 2 +- subworkflows/ssuissero/tests/main.nf.test.snap | 2 +- .../staphopiasccmec/tests/main.nf.test.snap | 2 +- subworkflows/staphscan/tests/main.nf.test.snap | 2 +- .../stecfinder/tests/main.nf.test.snap | 2 +- subworkflows/stxtyper/tests/main.nf.test.snap | 2 +- subworkflows/sylph/tests/main.nf.test.snap | 2 +- subworkflows/tblastn/tests/main.nf.test.snap | 2 +- subworkflows/tblastx/tests/main.nf.test.snap | 2 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- subworkflows/teton/tests/main.nf.test.snap | 2 +- subworkflows/traitar/tests/main.nf.test.snap | 2 +- tests/main.nf.test.snap | 18 +++++++++--------- versions.yml | 2 +- .../bactopia-tools/abricate/nextflow.config | 2 +- .../abricate/tests/main.nf.test.snap | 2 +- .../bactopia-tools/abritamr/nextflow.config | 2 +- .../abritamr/tests/main.nf.test.snap | 2 +- .../bactopia-tools/agrvate/nextflow.config | 2 +- .../agrvate/tests/main.nf.test.snap | 4 ++-- .../amrfinderplus/nextflow.config | 2 +- .../amrfinderplus/tests/main.nf.test.snap | 4 ++-- workflows/bactopia-tools/ariba/nextflow.config | 2 +- .../ariba/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/bakta/nextflow.config | 2 +- .../bakta/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/blastn/nextflow.config | 2 +- .../blastn/tests/main.nf.test.snap | 6 +++--- .../bactopia-tools/blastp/nextflow.config | 2 +- .../blastp/tests/main.nf.test.snap | 6 +++--- .../bactopia-tools/blastx/nextflow.config | 2 +- .../blastx/tests/main.nf.test.snap | 6 +++--- .../bactopia-tools/bracken/nextflow.config | 2 +- .../bracken/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/btyper3/nextflow.config | 2 +- .../btyper3/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/busco/nextflow.config | 2 +- .../busco/tests/main.nf.test.snap | 2 +- .../bactopia-tools/checkm/nextflow.config | 2 +- .../checkm/tests/main.nf.test.snap | 2 +- .../bactopia-tools/checkm2/nextflow.config | 2 +- .../checkm2/tests/main.nf.test.snap | 2 +- .../clermontyping/nextflow.config | 2 +- .../clermontyping/tests/main.nf.test.snap | 2 +- .../defensefinder/nextflow.config | 2 +- .../defensefinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ectyper/nextflow.config | 2 +- .../ectyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/eggnog/nextflow.config | 2 +- .../eggnog/tests/main.nf.test.snap | 2 +- .../bactopia-tools/emmtyper/nextflow.config | 2 +- .../emmtyper/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/fastani/nextflow.config | 2 +- .../fastani/tests/main.nf.test.snap | 6 +++--- workflows/bactopia-tools/gamma/nextflow.config | 2 +- .../gamma/tests/main.nf.test.snap | 2 +- .../bactopia-tools/genotyphi/nextflow.config | 2 +- .../bactopia-tools/genotyphi/tests/.nftignore | 1 + .../genotyphi/tests/main.nf.test.snap | 4 +--- .../bactopia-tools/gigatyper/nextflow.config | 2 +- .../gigatyper/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/gtdb/nextflow.config | 2 +- .../gtdb/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/hicap/nextflow.config | 2 +- .../hicap/tests/main.nf.test.snap | 2 +- .../bactopia-tools/hpsuissero/nextflow.config | 2 +- .../hpsuissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ismapper/nextflow.config | 2 +- .../ismapper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/kleborate/nextflow.config | 2 +- .../kleborate/tests/main.nf.test.snap | 2 +- .../bactopia-tools/kraken2/nextflow.config | 2 +- .../kraken2/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/legsta/nextflow.config | 2 +- .../legsta/tests/main.nf.test.snap | 2 +- .../bactopia-tools/lissero/nextflow.config | 2 +- .../lissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mashdist/nextflow.config | 2 +- .../mashdist/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mashtree/nextflow.config | 2 +- .../mashtree/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/mcroni/nextflow.config | 2 +- .../mcroni/tests/main.nf.test.snap | 2 +- .../bactopia-tools/meningotype/nextflow.config | 2 +- .../meningotype/tests/main.nf.test.snap | 2 +- .../bactopia-tools/merlin/nextflow.config | 2 +- .../merlin/tests/main.nf.test.snap | 4 ++-- workflows/bactopia-tools/midas/nextflow.config | 2 +- .../midas/tests/main.nf.test.snap | 4 ++-- workflows/bactopia-tools/mlst/nextflow.config | 2 +- .../mlst/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mobsuite/nextflow.config | 2 +- .../mobsuite/tests/main.nf.test.snap | 2 +- .../bactopia-tools/mykrobe/nextflow.config | 2 +- .../mykrobe/tests/main.nf.test.snap | 2 +- .../bactopia-tools/ngmaster/nextflow.config | 2 +- .../ngmaster/tests/main.nf.test.snap | 2 +- .../bactopia-tools/pangenome/nextflow.config | 2 +- .../pangenome/tests/main.nf.test.snap | 12 ++++++------ workflows/bactopia-tools/pasty/nextflow.config | 2 +- .../pasty/tests/main.nf.test.snap | 2 +- .../bactopia-tools/pbptyper/nextflow.config | 2 +- .../pbptyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/phispy/nextflow.config | 2 +- .../phispy/tests/main.nf.test.snap | 2 +- .../plasmidfinder/nextflow.config | 2 +- .../plasmidfinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/pneumocat/nextflow.config | 2 +- .../pneumocat/tests/main.nf.test.snap | 2 +- .../bactopia-tools/prokka/nextflow.config | 2 +- .../prokka/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/quast/nextflow.config | 2 +- .../quast/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/rgi/nextflow.config | 2 +- .../bactopia-tools/rgi/tests/main.nf.test.snap | 2 +- .../bactopia-tools/sccmec/nextflow.config | 2 +- .../sccmec/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/scrubber/nextflow.config | 2 +- .../scrubber/tests/main.nf.test.snap | 6 +++--- .../bactopia-tools/seqsero2/nextflow.config | 2 +- .../seqsero2/tests/main.nf.test.snap | 2 +- .../bactopia-tools/seroba/nextflow.config | 2 +- .../seroba/tests/main.nf.test.snap | 2 +- .../bactopia-tools/shigapass/nextflow.config | 2 +- .../shigapass/tests/main.nf.test.snap | 2 +- .../bactopia-tools/shigatyper/nextflow.config | 2 +- .../shigatyper/tests/main.nf.test.snap | 2 +- .../shigeifinder/nextflow.config | 2 +- .../shigeifinder/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/sistr/nextflow.config | 2 +- .../sistr/tests/main.nf.test.snap | 2 +- .../bactopia-tools/snippy/nextflow.config | 2 +- .../snippy/tests/main.nf.test.snap | 12 ++++++------ .../bactopia-tools/spatyper/nextflow.config | 2 +- .../spatyper/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/ssuissero/nextflow.config | 2 +- .../ssuissero/tests/main.nf.test.snap | 2 +- .../bactopia-tools/staphscan/nextflow.config | 2 +- .../staphscan/tests/main.nf.test.snap | 2 +- .../bactopia-tools/staphtyper/nextflow.config | 2 +- .../staphtyper/tests/main.nf.test.snap | 2 +- .../bactopia-tools/stecfinder/nextflow.config | 2 +- .../stecfinder/tests/main.nf.test.snap | 2 +- .../bactopia-tools/stxtyper/nextflow.config | 2 +- .../stxtyper/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/sylph/nextflow.config | 2 +- .../sylph/tests/main.nf.test.snap | 2 +- .../bactopia-tools/tblastn/nextflow.config | 2 +- .../tblastn/tests/main.nf.test.snap | 4 ++-- .../bactopia-tools/tblastx/nextflow.config | 2 +- .../tblastx/tests/main.nf.test.snap | 6 +++--- .../bactopia-tools/tbprofiler/nextflow.config | 2 +- .../tbprofiler/tests/main.nf.test.snap | 2 +- .../bactopia-tools/traitar/nextflow.config | 2 +- .../traitar/tests/main.nf.test.snap | 2 +- workflows/cleanyerreads/nextflow.config | 2 +- .../cleanyerreads/tests/main.nf.test.snap | 4 ++-- workflows/staphopia/nextflow.config | 2 +- workflows/staphopia/tests/main.nf.test.snap | 2 +- workflows/teton/nextflow.config | 2 +- workflows/teton/tests/main.nf.test.snap | 6 +++--- 348 files changed, 510 insertions(+), 505 deletions(-) diff --git a/.claude/docs/project/04-testing-framework.md b/.claude/docs/project/04-testing-framework.md index 6a43d99c8..843e35177 100644 --- a/.claude/docs/project/04-testing-framework.md +++ b/.claude/docs/project/04-testing-framework.md @@ -410,7 +410,7 @@ Sourced from `bactopia-test --help`: | `--outdir PATH` | Output | Where `logs/` is written | | `--json` | Output | Emit structured JSON summary | | `--keep` | Cleanup | Preserve `.nf-test/` dirs and logs on pass | -| `--cleanup` | Cleanup | Remove all `.nf-test/` temp dirs and exit (no tests run) | +| `--cleanup` | Cleanup | Remove `.nf-test/` temp dirs under `modules/`, `subworkflows/`, `workflows/`, `tests/` and exit (skips `logs/`; no tests run) | ### Raw `nf-test` (debugging) diff --git a/.claude/skills/run-tests/SKILL.md b/.claude/skills/run-tests/SKILL.md index a77af5577..f766c158c 100644 --- a/.claude/skills/run-tests/SKILL.md +++ b/.claude/skills/run-tests/SKILL.md @@ -209,7 +209,7 @@ Defaults in parentheses. - `--timeout` — per-test timeout in **minutes**, 0 to disable (default: 90) **Cleanup (operates instead of running tests)** -- `--cleanup` — find and remove all `.nf-test/` temp files, then exit +- `--cleanup` — remove `.nf-test/` temp files under `modules/`, `subworkflows/`, `workflows/`, `tests/`, then exit (skips `logs/` work dirs) - `--dry-run` — with `--cleanup`, list what would be removed **Output** diff --git a/CHANGELOG.md b/CHANGELOG.md index ae2db5a4d..b8f11da58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -73,6 +73,15 @@ sidebar_position: 5000 - `rgi_exclude_nudge` emitting the removed `--exclude_nudge` flag; replaced with `rgi_include_nudge` which passes RGI 6's opt-in `--include_nudge` - `bactopia datasets` tests requesting a version-pinned `mlst.tar.gz` (404); `mlst_url` has been version-less since v4.0.0 - `gubbins` failing under Singularity/Apptainer when Numba tried to write to read-only container ([#667](https://github.com/bactopia/bactopia/issues/667)) (@pvanheus) +- `agrvate`, `gamma`, and `traitar` modules failing under Conda with `cp: '...' are the same file` + when the staged input was copied onto its own path (used `fna.fileName.name` for the work-dir copy target) +- Conda profile tool_errors from unconstrained transitive dependencies (docker/singularity unaffected); pinned in each module's `ext.toolName`: + - `ariba`, `ismapper`, `mykrobe`, `shigeifinder`, `sistr` - `setuptools=80` (`pkg_resources` removed in setuptools 81) + - `clonalframeml` (maskrc-svg) - `python=3.12` (stdlib `cgi` removed in Python 3.13) + - `hicap` - `biopython=1.79` (`SeqFeature.strand` removed in Biopython 1.80) + - `mcroni` - `numpy=2.0` (`reshape(newshape=)` removed in NumPy 2.1) + - `clermontyping` - `r-readr=2.1` (`quoted_na` promoted to a hard error) + - `snippy` (bactopia-variants) - `htslib=1.14` (bcftools 1.14/htslib 1.21 ABI mismatch segfaulted `bcftools consensus`) ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 diff --git a/catalog.json b/catalog.json index adabeabed..3751824de 100644 --- a/catalog.json +++ b/catalog.json @@ -1,9 +1,9 @@ { "version": "1.0", - "generated": "2026-07-29T16:50:49Z", + "generated": "2026-08-04T18:35:56Z", "bactopia_version": "4.1.0", "bactopia_py_version": "2.3.0", - "nf_bactopia_version": "2.1.6", + "nf_bactopia_version": "2.1.7", "modules": { "abricate_run": { "description": "Mass screening of contigs for antimicrobial and virulence genes.", diff --git a/conf/test_base.config b/conf/test_base.config index 88083f3db..0e4bf00e2 100644 --- a/conf/test_base.config +++ b/conf/test_base.config @@ -22,5 +22,5 @@ params { // Plugin plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 26cd3f4bf..5fcfddf62 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -17,7 +17,7 @@ requirements: - python >3.9,<3.14 - wget run: - - bactopia-py >=2.3.0 + - bactopia-py >=2.4.0 - conda >=25 - coreutils - mamba >=2 diff --git a/modules/abricate/run/tests/main.nf.test.snap b/modules/abricate/run/tests/main.nf.test.snap index c1743a3f3..958ff84c9 100644 --- a/modules/abricate/run/tests/main.nf.test.snap +++ b/modules/abricate/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,7baef5ee36e4b70a7227723d89bf97ea" ] ], - "timestamp": "2026-07-30T00:27:33.430771963", + "timestamp": "2026-07-30T19:01:00.391837391", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abricate/summary/tests/main.nf.test.snap b/modules/abricate/summary/tests/main.nf.test.snap index 72defcfb4..e0c71575c 100644 --- a/modules/abricate/summary/tests/main.nf.test.snap +++ b/modules/abricate/summary/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,87422ca0c784de85ba93ac7352052d82" ] ], - "timestamp": "2026-07-30T00:27:37.80307685", + "timestamp": "2026-07-30T19:01:02.763625519", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/abritamr/run/tests/main.nf.test.snap b/modules/abritamr/run/tests/main.nf.test.snap index 339654465..4f056f664 100644 --- a/modules/abritamr/run/tests/main.nf.test.snap +++ b/modules/abritamr/run/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-30T00:31:50.164649198", + "timestamp": "2026-07-30T19:05:13.996504626", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,752ffc1de1fcfed0f5e5bb025b542fdd" ] ], - "timestamp": "2026-07-30T00:36:04.650621711", + "timestamp": "2026-07-30T19:09:37.004458976", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf index 88b39cb7c..b2b2fae52 100644 --- a/modules/agrvate/main.nf +++ b/modules/agrvate/main.nf @@ -69,14 +69,14 @@ process AGRVATE { process_name: task.ext.process_name ) - def is_compressed = fna.getName().endsWith(".gz") ? true : false - def fna_name = fna.getName().replace(".gz", "") + def is_compressed = fna.fileName.name.endsWith(".gz") ? true : false + def fna_name = fna.fileName.name.replace(".gz", "") """ if [ "${is_compressed}" == "true" ]; then gzip -c -d ${fna} > ./${fna_name} else # agrvate does not support symlinks - cp ${fna} ./${fna_name} + cp -L ${fna} ./${fna_name} fi agrvate \\ @@ -88,9 +88,7 @@ process AGRVATE { mv supplemental/${prefix}-summary.tab ./${prefix}.tsv # Cleanup - if [ "${is_compressed}" == "true" ]; then - rm -rf ${fna_name} - fi + rm -rf ./${fna_name} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/agrvate/tests/main.nf.test.snap b/modules/agrvate/tests/main.nf.test.snap index 49d07971c..eb5289f7e 100644 --- a/modules/agrvate/tests/main.nf.test.snap +++ b/modules/agrvate/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-30T00:27:45.78711724", + "timestamp": "2026-07-30T19:01:13.333516992", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fbf8f6ba5629f99370082f5f837a7a2e" ] ], - "timestamp": "2026-07-30T00:27:30.771873199", + "timestamp": "2026-07-30T19:00:59.980438821", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/amrfinderplus/run/tests/main.nf.test.snap b/modules/amrfinderplus/run/tests/main.nf.test.snap index 1c8162544..346c72c93 100644 --- a/modules/amrfinderplus/run/tests/main.nf.test.snap +++ b/modules/amrfinderplus/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-30T00:27:39.164054105", + "timestamp": "2026-07-30T19:01:11.923262811", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b34cfaa3dacca27f98634ce626aab7df" ] ], - "timestamp": "2026-07-30T00:28:02.254823537", + "timestamp": "2026-07-30T19:01:34.662980606", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ariba/getref/module.config b/modules/ariba/getref/module.config index 519e8a94e..310e13494 100644 --- a/modules/ariba/getref/module.config +++ b/modules/ariba/getref/module.config @@ -15,7 +15,7 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::ariba=2.14.7".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::ariba=2.14.7 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/ariba:2.14.7--py39h746d604_0" ext.image = "https://depot.galaxyproject.org/singularity/ariba:2.14.7--py39h746d604_0" ext.condaDir = "${params.condadir}" diff --git a/modules/ariba/run/module.config b/modules/ariba/run/module.config index c04c7cfdd..991726f69 100644 --- a/modules/ariba/run/module.config +++ b/modules/ariba/run/module.config @@ -39,7 +39,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::ariba=2.14.7".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::ariba=2.14.7 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/ariba:2.14.7--py39h746d604_0" ext.image = "https://depot.galaxyproject.org/singularity/ariba:2.14.7--py39h746d604_0" ext.condaDir = "${params.condadir}" diff --git a/modules/ariba/run/tests/main.nf.test.snap b/modules/ariba/run/tests/main.nf.test.snap index 2cae6a94a..b4acf088a 100644 --- a/modules/ariba/run/tests/main.nf.test.snap +++ b/modules/ariba/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2d20a87ab1578332cae79c947a52e8f8" ] ], - "timestamp": "2026-07-30T00:28:25.295295632", + "timestamp": "2026-07-30T19:01:48.501156944", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/assembler/tests/main.nf.test.snap b/modules/bactopia/assembler/tests/main.nf.test.snap index a82a0f283..65b01a37d 100644 --- a/modules/bactopia/assembler/tests/main.nf.test.snap +++ b/modules/bactopia/assembler/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:43:04.309806358", + "timestamp": "2026-07-30T19:17:06.857512715", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:49:46.54340004", + "timestamp": "2026-07-30T19:23:20.256569677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:49:02.152014818", + "timestamp": "2026-07-30T19:22:40.875565491", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:46:56.905269041", + "timestamp": "2026-07-30T19:20:36.677813837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -98,7 +98,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:47:41.368206613", + "timestamp": "2026-07-30T19:21:18.12930881", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -119,7 +119,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:29:57.965081441", + "timestamp": "2026-07-30T19:03:23.888754747", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:30:36.673420092", + "timestamp": "2026-07-30T19:04:04.211041576", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -161,7 +161,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:34:18.063960274", + "timestamp": "2026-07-30T19:08:17.703593976", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/gather/tests/main.nf.test.snap b/modules/bactopia/gather/tests/main.nf.test.snap index 40798ef3a..78c15ec81 100644 --- a/modules/bactopia/gather/tests/main.nf.test.snap +++ b/modules/bactopia/gather/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:28:30.680970188", + "timestamp": "2026-07-30T19:02:05.469986376", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:28:54.243545308", + "timestamp": "2026-07-30T19:02:28.432278438", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -70,7 +70,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:30:31.639769887", + "timestamp": "2026-07-30T19:04:02.535874545", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:30:12.165437052", + "timestamp": "2026-07-30T19:03:43.552805995", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -121,7 +121,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:29:29.44934561", + "timestamp": "2026-07-30T19:03:01.490354819", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:29:51.043793603", + "timestamp": "2026-07-30T19:03:22.422035436", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -173,7 +173,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:27:44.840771684", + "timestamp": "2026-07-30T19:01:21.591931572", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -199,7 +199,7 @@ "versions.yml:md5,92a16e28a5dc385e3e050bae94c9d4ef" ] ], - "timestamp": "2026-07-30T00:28:07.005802392", + "timestamp": "2026-07-30T19:01:43.359870539", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/qc/tests/main.nf.test.snap b/modules/bactopia/qc/tests/main.nf.test.snap index 93279d1ae..64b3aa55c 100644 --- a/modules/bactopia/qc/tests/main.nf.test.snap +++ b/modules/bactopia/qc/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:29:03.659398485", + "timestamp": "2026-07-30T19:02:27.03483307", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:30:04.521158614", + "timestamp": "2026-07-30T19:03:27.769846657", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:32:40.710016356", + "timestamp": "2026-07-30T19:06:04.95777414", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:30:51.266979238", + "timestamp": "2026-07-30T19:04:14.917296416", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -98,7 +98,7 @@ "species": "Portiera aleyrodidarum" } ], - "timestamp": "2026-07-30T00:33:22.799446708", + "timestamp": "2026-07-30T19:06:43.129431936", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/sketcher/tests/main.nf.test.snap b/modules/bactopia/sketcher/tests/main.nf.test.snap index f0aaa9de8..a75c26a10 100644 --- a/modules/bactopia/sketcher/tests/main.nf.test.snap +++ b/modules/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,559fcd38f7410952b8da3f25f165d6fd" ] ], - "timestamp": "2026-07-30T00:30:16.285079051", + "timestamp": "2026-07-30T19:03:44.161949329", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bactopia/teton/tests/main.nf.test.snap b/modules/bactopia/teton/tests/main.nf.test.snap index 8c307fde3..982601b8a 100644 --- a/modules/bactopia/teton/tests/main.nf.test.snap +++ b/modules/bactopia/teton/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-30T00:27:42.124626112", + "timestamp": "2026-07-30T19:01:01.796760179", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -43,7 +43,7 @@ "versions.yml:md5,7b812154dd8f427d515417e5cfa98423" ] ], - "timestamp": "2026-07-30T00:27:57.82836261", + "timestamp": "2026-07-30T19:01:16.865011628", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bakta/run/tests/main.nf.test.snap b/modules/bakta/run/tests/main.nf.test.snap index 10d303bee..0382cdb29 100644 --- a/modules/bakta/run/tests/main.nf.test.snap +++ b/modules/bakta/run/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-30T00:31:33.386526961", + "timestamp": "2026-07-30T19:05:08.727846161", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,370f7613e15ca17b54474b6c92316d6c" ] ], - "timestamp": "2026-07-30T00:34:20.087738169", + "timestamp": "2026-07-30T19:08:02.3833008", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastn/tests/main.nf.test.snap b/modules/blast/blastn/tests/main.nf.test.snap index f7ebe288e..4aeb42fec 100644 --- a/modules/blast/blastn/tests/main.nf.test.snap +++ b/modules/blast/blastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,45d0dac48620078713131f03b02bd14a" ] ], - "timestamp": "2026-07-30T00:27:30.248901271", + "timestamp": "2026-07-30T19:01:01.860442122", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastp/tests/main.nf.test.snap b/modules/blast/blastp/tests/main.nf.test.snap index dceaf21c1..1a414eb8a 100644 --- a/modules/blast/blastp/tests/main.nf.test.snap +++ b/modules/blast/blastp/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,617451a4191edeef7d2c7fb101c1ac14" ] ], - "timestamp": "2026-07-30T00:27:30.370813436", + "timestamp": "2026-07-30T19:01:01.585693627", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/blastx/tests/main.nf.test.snap b/modules/blast/blastx/tests/main.nf.test.snap index 1a37f6c1c..647f26734 100644 --- a/modules/blast/blastx/tests/main.nf.test.snap +++ b/modules/blast/blastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6a3a4c2a4204ac747af921720f265d86" ] ], - "timestamp": "2026-07-30T00:27:36.683267065", + "timestamp": "2026-07-30T19:01:05.844155633", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastn/tests/main.nf.test.snap b/modules/blast/tblastn/tests/main.nf.test.snap index 111b7947e..904ea1638 100644 --- a/modules/blast/tblastn/tests/main.nf.test.snap +++ b/modules/blast/tblastn/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,24c7db9cd7b317dcf8ad2057a04b2860" ] ], - "timestamp": "2026-07-30T00:27:30.442772949", + "timestamp": "2026-07-30T19:01:00.704641483", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/blast/tblastx/tests/main.nf.test.snap b/modules/blast/tblastx/tests/main.nf.test.snap index 0cc347d12..10d8fc7df 100644 --- a/modules/blast/tblastx/tests/main.nf.test.snap +++ b/modules/blast/tblastx/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2d402efb20baa10e7b3af88ef3f2312d" ] ], - "timestamp": "2026-07-30T00:27:32.057380628", + "timestamp": "2026-07-30T19:01:10.570704095", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/bracken/tests/main.nf.test.snap b/modules/bracken/tests/main.nf.test.snap index 9e228543a..d8b036b8a 100644 --- a/modules/bracken/tests/main.nf.test.snap +++ b/modules/bracken/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "SRR2838702.kraken2.report.txt:md5,29a9ad9bb9b9b17a43e969f82c6e3e9f", "SRR2838702.bracken.report.txt:md5,3ca9ddfeb074bce0b9fd1e8b8b9c8443" ], - "timestamp": "2026-07-30T00:28:11.754359711", + "timestamp": "2026-07-30T19:01:31.941954637", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "SRR2838702.kraken2.report.txt:md5,d883be153ee044e74a9504c128f20ccd", "SRR2838702.bracken.report.txt:md5,2ed70b1d772694c9737e5c817efd2d97" ], - "timestamp": "2026-07-30T00:31:45.290162074", + "timestamp": "2026-07-30T19:05:08.82532146", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/btyper3/tests/main.nf.test.snap b/modules/btyper3/tests/main.nf.test.snap index 656c5d4dc..0efdbf299 100644 --- a/modules/btyper3/tests/main.nf.test.snap +++ b/modules/btyper3/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-30T00:31:19.049715808", + "timestamp": "2026-07-30T19:04:42.381040781", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d417e0067e48969f3cc66f12727471ba" ] ], - "timestamp": "2026-07-30T00:29:27.177510154", + "timestamp": "2026-07-30T19:02:46.436132943", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/busco/tests/main.nf.test.snap b/modules/busco/tests/main.nf.test.snap index 93645a981..c0fd5c1c9 100644 --- a/modules/busco/tests/main.nf.test.snap +++ b/modules/busco/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-30T00:28:37.885132821", + "timestamp": "2026-07-30T19:02:00.498495737", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,63a54671479080ef196761c11a1d1ee9" ] ], - "timestamp": "2026-07-30T00:28:00.420520931", + "timestamp": "2026-07-30T19:01:23.518262947", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm/lineagewf/tests/main.nf.test.snap b/modules/checkm/lineagewf/tests/main.nf.test.snap index 13bdfe4da..3db817e54 100644 --- a/modules/checkm/lineagewf/tests/main.nf.test.snap +++ b/modules/checkm/lineagewf/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-30T00:36:14.74113468", + "timestamp": "2026-07-30T19:10:50.721728279", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,26aa8d1005c5ccafccfe332302d24f80" ] ], - "timestamp": "2026-07-30T00:38:33.400832662", + "timestamp": "2026-07-30T19:12:42.276902775", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/checkm2/predict/tests/main.nf.test.snap b/modules/checkm2/predict/tests/main.nf.test.snap index 1e283e796..35bbd8b0f 100644 --- a/modules/checkm2/predict/tests/main.nf.test.snap +++ b/modules/checkm2/predict/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-30T00:36:57.527565395", + "timestamp": "2026-07-30T19:10:34.905820971", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195" ] ], - "timestamp": "2026-07-30T00:32:33.598548885", + "timestamp": "2026-07-30T19:06:07.118903521", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clermontyping/module.config b/modules/clermontyping/module.config index 0a37032d2..f3a572271 100644 --- a/modules/clermontyping/module.config +++ b/modules/clermontyping/module.config @@ -17,7 +17,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::clermontyping=24.02".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::clermontyping=24.02 conda-forge::r-readr=2.1".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/clermontyping:24.02--py312hdfd78af_1" ext.image = "https://depot.galaxyproject.org/singularity/clermontyping:24.02--py312hdfd78af_1" ext.condaDir = "${params.condadir}" diff --git a/modules/clermontyping/tests/main.nf.test.snap b/modules/clermontyping/tests/main.nf.test.snap index ef81ba646..8f36aa746 100644 --- a/modules/clermontyping/tests/main.nf.test.snap +++ b/modules/clermontyping/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-30T00:28:33.70061174", + "timestamp": "2026-07-30T19:01:59.804010965", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f4bd87be75db967a591cbfaef55ad136" ] ], - "timestamp": "2026-07-30T00:27:52.24623652", + "timestamp": "2026-07-30T19:01:18.809092664", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/clonalframeml/module.config b/modules/clonalframeml/module.config index feb4fda16..aa56e4cb7 100644 --- a/modules/clonalframeml/module.config +++ b/modules/clonalframeml/module.config @@ -20,7 +20,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::clonalframeml=1.12 bioconda::maskrc-svg=0.5".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::clonalframeml=1.12 bioconda::maskrc-svg=0.5 conda-forge::python=3.12".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/mulled-v2-f5c68f1508671d5744655da9b0e8b609098f4138:7e089189af7822a6a18245830639dbfe11a4c277-0" ext.image = "https://depot.galaxyproject.org/singularity/mulled-v2-f5c68f1508671d5744655da9b0e8b609098f4138:7e089189af7822a6a18245830639dbfe11a4c277-0" ext.condaDir = "${params.condadir}" diff --git a/modules/clonalframeml/tests/main.nf.test.snap b/modules/clonalframeml/tests/main.nf.test.snap index e04371fdb..c5bb6da41 100644 --- a/modules/clonalframeml/tests/main.nf.test.snap +++ b/modules/clonalframeml/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-30T00:28:40.41245868", + "timestamp": "2026-07-30T19:02:18.126742578", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,34acb1ed178173aa1445f1f0a9238e64" ] ], - "timestamp": "2026-07-30T00:30:01.468282979", + "timestamp": "2026-07-30T19:03:39.064087697", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/concat/tests/main.nf.test.snap b/modules/csvtk/concat/tests/main.nf.test.snap index 7f3cf7800..7dc2f21d5 100644 --- a/modules/csvtk/concat/tests/main.nf.test.snap +++ b/modules/csvtk/concat/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-30T00:27:41.403303919", + "timestamp": "2026-07-30T19:01:06.99317976", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,c203a84cc5b289951b70302549dcf08d" ] ], - "timestamp": "2026-07-30T00:27:56.136849312", + "timestamp": "2026-07-30T19:01:22.210365652", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/csvtk/join/tests/main.nf.test.snap b/modules/csvtk/join/tests/main.nf.test.snap index 87bc3e4ff..6e621acea 100644 --- a/modules/csvtk/join/tests/main.nf.test.snap +++ b/modules/csvtk/join/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-30T00:27:30.034340654", + "timestamp": "2026-07-30T19:00:59.285867921", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,b80d80628bb39bba336cff32fe502aac" ] ], - "timestamp": "2026-07-30T00:27:44.265091067", + "timestamp": "2026-07-30T19:01:12.091971745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/deacon/filter/tests/main.nf.test.snap b/modules/deacon/filter/tests/main.nf.test.snap index 182855ba3..92ba46cce 100644 --- a/modules/deacon/filter/tests/main.nf.test.snap +++ b/modules/deacon/filter/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-30T00:29:08.229204515", + "timestamp": "2026-07-30T19:02:31.608511666", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-30T00:28:32.499144526", + "timestamp": "2026-07-30T19:01:57.161551068", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,7b45b6c5acaead3263ddcf10a6b7b1c3" ] ], - "timestamp": "2026-07-30T00:28:00.223385522", + "timestamp": "2026-07-30T19:01:25.369991526", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/defensefinder/run/tests/main.nf.test.snap b/modules/defensefinder/run/tests/main.nf.test.snap index 7af560d42..ff8b74454 100644 --- a/modules/defensefinder/run/tests/main.nf.test.snap +++ b/modules/defensefinder/run/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,96378138554cc40b07841aed5efb3e7d" ] ], - "timestamp": "2026-07-30T00:28:20.926954356", + "timestamp": "2026-07-30T19:01:39.151339268", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ectyper/tests/main.nf.test.snap b/modules/ectyper/tests/main.nf.test.snap index 013c43ed9..383144dbf 100644 --- a/modules/ectyper/tests/main.nf.test.snap +++ b/modules/ectyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-30T00:28:33.264034136", + "timestamp": "2026-07-30T19:02:07.337367191", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,8da5d25c63ebd770e9c1776106725972" ] ], - "timestamp": "2026-07-30T00:27:54.928583655", + "timestamp": "2026-07-30T19:01:30.096476215", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/eggnog/mapper/tests/main.nf.test.snap b/modules/eggnog/mapper/tests/main.nf.test.snap index 03f777ac1..5b94aba1a 100644 --- a/modules/eggnog/mapper/tests/main.nf.test.snap +++ b/modules/eggnog/mapper/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "sample" } ], - "timestamp": "2026-07-30T00:47:20.595133302", + "timestamp": "2026-07-30T19:15:27.85648084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -27,7 +27,7 @@ "scope": "sample" } ], - "timestamp": "2026-07-30T00:53:03.419968224", + "timestamp": "2026-07-30T19:21:08.051829481", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/emmtyper/tests/main.nf.test.snap b/modules/emmtyper/tests/main.nf.test.snap index f5afb9a65..8208d216d 100644 --- a/modules/emmtyper/tests/main.nf.test.snap +++ b/modules/emmtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-30T00:28:03.01572836", + "timestamp": "2026-07-30T19:01:15.516758295", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-30T00:28:18.255092721", + "timestamp": "2026-07-30T19:01:31.61507558", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,8028be40b22a6bec2ce48bbc811c663a" ] ], - "timestamp": "2026-07-30T00:27:45.825260672", + "timestamp": "2026-07-30T19:00:59.825790299", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/fastani/tests/main.nf.test.snap b/modules/fastani/tests/main.nf.test.snap index 06b4e3aa8..9add115c1 100644 --- a/modules/fastani/tests/main.nf.test.snap +++ b/modules/fastani/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-30T00:27:34.015623035", + "timestamp": "2026-07-30T19:00:59.602119388", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3c8fce061d0dc503f4830ad0f1e2ebba" ] ], - "timestamp": "2026-07-30T00:27:48.801306304", + "timestamp": "2026-07-30T19:01:13.170212084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gamma/main.nf b/modules/gamma/main.nf index 1a8176c5c..7b1c982e1 100644 --- a/modules/gamma/main.nf +++ b/modules/gamma/main.nf @@ -77,8 +77,8 @@ process GAMMA { process_name: task.ext.process_name ) - def is_compressed = fna.getName().endsWith(".gz") ? true : false - def fna_name = fna.getName().replace(".gz", "") + def is_compressed = fna.fileName.name.endsWith(".gz") ? true : false + def fna_name = fna.fileName.name.replace(".gz", "") // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def VERSION = '2.1' @@ -86,7 +86,7 @@ process GAMMA { if [ "${is_compressed}" == "true" ]; then gzip -c -d ${fna} > ./${fna_name} else - cp ${fna} ./${fna_name} + cp -L ${fna} ./${fna_name} fi GAMMA.py \\ @@ -96,9 +96,7 @@ process GAMMA { ${prefix} # Cleanup - if [ "${is_compressed}" == "true" ]; then - rm -rf ${fna_name} - fi + rm -rf ./${fna_name} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/gamma/tests/main.nf.test.snap b/modules/gamma/tests/main.nf.test.snap index ca2dd8747..29d27a34c 100644 --- a/modules/gamma/tests/main.nf.test.snap +++ b/modules/gamma/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-30T00:27:41.680062691", + "timestamp": "2026-07-30T19:01:12.592848128", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,11f61b65b031ac9b3e1afcd127b93d49" ] ], - "timestamp": "2026-07-30T00:27:56.88346073", + "timestamp": "2026-07-30T19:01:28.026426906", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genomedl/tests/main.nf.test.snap b/modules/genomedl/tests/main.nf.test.snap index e8e708e9d..a177a3dd9 100644 --- a/modules/genomedl/tests/main.nf.test.snap +++ b/modules/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-30T00:28:04.222812434", + "timestamp": "2026-07-30T19:01:27.973113225", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-30T00:27:45.824303281", + "timestamp": "2026-07-30T19:01:08.996012109", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,bb83b7d6091b1b7e8a93fba8cc9a3e7d" ] ], - "timestamp": "2026-07-30T00:28:22.029631151", + "timestamp": "2026-07-30T19:01:44.533547638", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/genotyphi/parse/module.config b/modules/genotyphi/parse/module.config index 33d9f9116..1048323a0 100644 --- a/modules/genotyphi/parse/module.config +++ b/modules/genotyphi/parse/module.config @@ -42,7 +42,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::mykrobe=0.13.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::mykrobe=0.13.0 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/mykrobe:0.13.0--py38h2214202_0" ext.image = "https://depot.galaxyproject.org/singularity/mykrobe:0.13.0--py38h2214202_0" ext.condaDir = "${params.condadir}" diff --git a/modules/genotyphi/parse/tests/main.nf.test.snap b/modules/genotyphi/parse/tests/main.nf.test.snap index e092eb6e2..d8dcbe5ce 100644 --- a/modules/genotyphi/parse/tests/main.nf.test.snap +++ b/modules/genotyphi/parse/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,359680888d6e4e84784879e6e92c3439" ] ], - "timestamp": "2026-07-30T00:27:35.802400406", + "timestamp": "2026-07-30T19:00:58.901288242", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gigatyper/tests/main.nf.test.snap b/modules/gigatyper/tests/main.nf.test.snap index c1c9e5e88..b418d37ec 100644 --- a/modules/gigatyper/tests/main.nf.test.snap +++ b/modules/gigatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ae98787b0c6ddf8f10515b895570a41a" ] ], - "timestamp": "2026-07-30T00:27:50.37761076", + "timestamp": "2026-07-30T19:01:14.005166773", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/gtdbtk/classifywf/tests/main.nf.test.snap index 4984b081b..9bb08aaab 100644 --- a/modules/gtdbtk/classifywf/tests/main.nf.test.snap +++ b/modules/gtdbtk/classifywf/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,7cb27f0b82d34e40565279ff91f60fda" ] ], - "timestamp": "2026-07-30T00:32:22.666239454", + "timestamp": "2026-07-30T19:06:03.495274325", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/gubbins/tests/main.nf.test.snap b/modules/gubbins/tests/main.nf.test.snap index 4ff212d93..dd74208af 100644 --- a/modules/gubbins/tests/main.nf.test.snap +++ b/modules/gubbins/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719" ], - "timestamp": "2026-07-30T00:28:31.765803438", + "timestamp": "2026-07-30T19:01:52.976881269", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -29,7 +29,7 @@ }, "test.masked.aln.gz:md5,0aa89f5b52d36f88d6bbf52b9015a719" ], - "timestamp": "2026-07-30T00:29:33.303400589", + "timestamp": "2026-07-30T19:02:56.185234141", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hicap/module.config b/modules/hicap/module.config index fee8233be..9909d7dda 100644 --- a/modules/hicap/module.config +++ b/modules/hicap/module.config @@ -27,7 +27,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::hicap=1.0.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::hicap=1.0.4 conda-forge::biopython=1.79".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/hicap:1.0.4--pyhdfd78af_2" ext.image = "https://depot.galaxyproject.org/singularity/hicap:1.0.4--pyhdfd78af_2" ext.condaDir = "${params.condadir}" diff --git a/modules/hicap/tests/main.nf.test.snap b/modules/hicap/tests/main.nf.test.snap index 19bff0a9b..5a7b42edd 100644 --- a/modules/hicap/tests/main.nf.test.snap +++ b/modules/hicap/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-30T00:28:48.718747423", + "timestamp": "2026-07-30T19:02:06.883246191", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-30T00:28:09.002534693", + "timestamp": "2026-07-30T19:01:27.129799543", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-30T00:30:00.282551315", + "timestamp": "2026-07-30T19:03:20.732689084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -77,7 +77,7 @@ "versions.yml:md5,a4a5a455027f57fbd081f501832ec3d3" ] ], - "timestamp": "2026-07-30T00:29:25.433950184", + "timestamp": "2026-07-30T19:02:44.146624378", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/hpsuissero/tests/main.nf.test.snap b/modules/hpsuissero/tests/main.nf.test.snap index 5cf0914bc..ad46a6e91 100644 --- a/modules/hpsuissero/tests/main.nf.test.snap +++ b/modules/hpsuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-30T00:27:50.398344313", + "timestamp": "2026-07-30T19:01:14.597731705", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2e1e831c688899545872927bdf90d852" ] ], - "timestamp": "2026-07-30T00:27:35.343292208", + "timestamp": "2026-07-30T19:01:00.300979516", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/iqtree/tests/main.nf.test.snap b/modules/iqtree/tests/main.nf.test.snap index 32822f0a0..5b2e413ee 100644 --- a/modules/iqtree/tests/main.nf.test.snap +++ b/modules/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-30T00:28:02.824648445", + "timestamp": "2026-07-30T19:01:24.814474762", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,e866b0d7c6f535259cd190571ebec653" ] ], - "timestamp": "2026-07-30T00:27:46.468835351", + "timestamp": "2026-07-30T19:01:08.606761219", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ismapper/module.config b/modules/ismapper/module.config index c57d6b261..4edcea125 100644 --- a/modules/ismapper/module.config +++ b/modules/ismapper/module.config @@ -36,7 +36,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::ismapper=2.0.2".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::ismapper=2.0.2 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/ismapper:2.0.2--pyhdfd78af_1" ext.image = "https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1" ext.condaDir = "${params.condadir}" diff --git a/modules/ismapper/tests/main.nf.test.snap b/modules/ismapper/tests/main.nf.test.snap index 49d4802a3..f89dd1edb 100644 --- a/modules/ismapper/tests/main.nf.test.snap +++ b/modules/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,bbe2280116459026bfc2304b2b6c0f5f" ] ], - "timestamp": "2026-07-30T00:28:22.059010483", + "timestamp": "2026-07-30T19:02:01.544785645", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kleborate/tests/main.nf.test.snap b/modules/kleborate/tests/main.nf.test.snap index c7ca09cd5..d1ae363c4 100644 --- a/modules/kleborate/tests/main.nf.test.snap +++ b/modules/kleborate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9511fd36659702fc20722109151dca4b" ] ], - "timestamp": "2026-07-30T00:28:03.978714127", + "timestamp": "2026-07-30T19:01:31.638304898", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/kraken2/tests/main.nf.test.snap b/modules/kraken2/tests/main.nf.test.snap index c7403a058..9120222d7 100644 --- a/modules/kraken2/tests/main.nf.test.snap +++ b/modules/kraken2/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-30T00:31:40.440445989", + "timestamp": "2026-07-30T19:05:04.105362641", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,d4763c91677a2c1d143fd4afd6ee8c4c" ] ], - "timestamp": "2026-07-30T00:28:08.604957494", + "timestamp": "2026-07-30T19:01:28.812358446", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/legsta/tests/main.nf.test.snap b/modules/legsta/tests/main.nf.test.snap index 264038c8d..832861300 100644 --- a/modules/legsta/tests/main.nf.test.snap +++ b/modules/legsta/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1ea80a08aa0a9efc6d82ffa9e668ad6d" ] ], - "timestamp": "2026-07-30T00:27:33.236665072", + "timestamp": "2026-07-30T19:00:59.971048627", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/lissero/tests/main.nf.test.snap b/modules/lissero/tests/main.nf.test.snap index 4400634bb..88cf0e0e2 100644 --- a/modules/lissero/tests/main.nf.test.snap +++ b/modules/lissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-30T00:27:49.542026847", + "timestamp": "2026-07-30T19:01:29.728833737", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,ab0e6efb3af123eb9bb0f6fdf60cac2f" ] ], - "timestamp": "2026-07-30T00:27:32.933525251", + "timestamp": "2026-07-30T19:01:12.614261239", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mash/dist/tests/main.nf.test.snap b/modules/mash/dist/tests/main.nf.test.snap index 922b5985d..924f8ca39 100644 --- a/modules/mash/dist/tests/main.nf.test.snap +++ b/modules/mash/dist/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-30T00:27:45.316719659", + "timestamp": "2026-07-30T19:01:18.974907865", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,fcbb8bfc66b899b46ba971030f287212" ] ], - "timestamp": "2026-07-30T00:27:30.975255211", + "timestamp": "2026-07-30T19:01:04.733521704", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mashtree/tests/main.nf.test.snap b/modules/mashtree/tests/main.nf.test.snap index 0af15d148..9c2b88e3b 100644 --- a/modules/mashtree/tests/main.nf.test.snap +++ b/modules/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,6d51bcb025e39e73864f2236b1ce99e9" ] ], - "timestamp": "2026-07-30T00:27:34.300206931", + "timestamp": "2026-07-30T19:01:02.067594861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mcroni/module.config b/modules/mcroni/module.config index 5a03a44dc..de33eb40a 100644 --- a/modules/mcroni/module.config +++ b/modules/mcroni/module.config @@ -14,7 +14,7 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::mcroni=1.0.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::mcroni=1.0.4 conda-forge::numpy=2.0".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/mcroni:1.0.4--pyh5e36f6f_0" ext.image = "https://depot.galaxyproject.org/singularity/mcroni:1.0.4--pyh5e36f6f_0" ext.condaDir = "${params.condadir}" diff --git a/modules/mcroni/tests/main.nf.test.snap b/modules/mcroni/tests/main.nf.test.snap index 46fae15d9..32b6f66b7 100644 --- a/modules/mcroni/tests/main.nf.test.snap +++ b/modules/mcroni/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-30T00:27:47.350368123", + "timestamp": "2026-07-30T19:01:16.968734334", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910" ] ], - "timestamp": "2026-07-30T00:27:30.714177546", + "timestamp": "2026-07-30T19:01:01.499110844", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/meningotype/tests/main.nf.test.snap b/modules/meningotype/tests/main.nf.test.snap index 11d8672cb..e04a5d115 100644 --- a/modules/meningotype/tests/main.nf.test.snap +++ b/modules/meningotype/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-30T00:27:55.96254851", + "timestamp": "2026-07-30T19:01:22.875551398", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,8d3bfe53cfc5fc586e9dd9fba13d374e" ] ], - "timestamp": "2026-07-30T00:27:38.424258563", + "timestamp": "2026-07-30T19:01:05.203558481", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/merlin/dist/tests/main.nf.test.snap b/modules/merlin/dist/tests/main.nf.test.snap index 7317ef9d4..dff730104 100644 --- a/modules/merlin/dist/tests/main.nf.test.snap +++ b/modules/merlin/dist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-30T00:28:57.416946521", + "timestamp": "2026-07-30T19:02:07.458443286", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,44524f1e9fb05faa952755ecf34bcd18" ] ], - "timestamp": "2026-07-30T00:30:16.561889489", + "timestamp": "2026-07-30T19:03:16.908045685", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/midas/species/tests/main.nf.test.snap b/modules/midas/species/tests/main.nf.test.snap index 2da6bfe04..2a6578a9d 100644 --- a/modules/midas/species/tests/main.nf.test.snap +++ b/modules/midas/species/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-30T00:34:37.316406256", + "timestamp": "2026-07-30T19:08:04.666523771", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,580a248b19c50e578df537679c14f459" ] ], - "timestamp": "2026-07-30T00:35:28.238972692", + "timestamp": "2026-07-30T19:08:58.728415642", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mlst/tests/main.nf.test.snap b/modules/mlst/tests/main.nf.test.snap index bb6445264..eb149fe9f 100644 --- a/modules/mlst/tests/main.nf.test.snap +++ b/modules/mlst/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,6515f9242cdb83b9c720f39ce67a528f" ] ], - "timestamp": "2026-07-30T00:27:45.810778893", + "timestamp": "2026-07-30T19:01:04.724308312", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mobsuite/recon/tests/main.nf.test.snap b/modules/mobsuite/recon/tests/main.nf.test.snap index fe546d9de..165ee33e2 100644 --- a/modules/mobsuite/recon/tests/main.nf.test.snap +++ b/modules/mobsuite/recon/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-30T00:31:45.827171744", + "timestamp": "2026-07-30T19:05:12.197818243", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -40,7 +40,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-30T00:30:41.901408002", + "timestamp": "2026-07-30T19:04:07.812256834", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,ff6f105fca429e7482ac358949a11f93" ] ], - "timestamp": "2026-07-30T00:29:10.044478174", + "timestamp": "2026-07-30T19:02:33.098847623", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/mykrobe/predict/module.config b/modules/mykrobe/predict/module.config index d0cd602f9..6e24a498b 100644 --- a/modules/mykrobe/predict/module.config +++ b/modules/mykrobe/predict/module.config @@ -26,7 +26,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::mykrobe=0.13.0".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::mykrobe=0.13.0 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/mykrobe:0.13.0--py312h20b014d_5" ext.image = "https://depot.galaxyproject.org/singularity/mykrobe:0.13.0--py312h20b014d_5" ext.condaDir = "${params.condadir}" diff --git a/modules/mykrobe/predict/tests/main.nf.test b/modules/mykrobe/predict/tests/main.nf.test index 7acfa4805..11f88bd92 100644 --- a/modules/mykrobe/predict/tests/main.nf.test +++ b/modules/mykrobe/predict/tests/main.nf.test @@ -31,12 +31,16 @@ nextflow_process { def record = process.out[0][0] assertAll( { assert process.success }, + // Reproducible outputs { assert snapshot( record.meta, - record.csv, - record.json, record.versions - ).match() } + ).match() }, + // Non-reproducible outputs + { assert [ + record.csv, + record.json + ].every { path(it).exists() } } ) } } diff --git a/modules/mykrobe/predict/tests/main.nf.test.snap b/modules/mykrobe/predict/tests/main.nf.test.snap index 600eaf1f7..97c7e3575 100644 --- a/modules/mykrobe/predict/tests/main.nf.test.snap +++ b/modules/mykrobe/predict/tests/main.nf.test.snap @@ -10,13 +10,11 @@ "scope": "sample", "single_end": false }, - "SRR2838702.csv:md5,a27c093fe0789e56a7100d16ae757766", - "SRR2838702.json:md5,c27fd2ccc9ffc107511fa83ef4920897", [ "versions.yml:md5,3756fdfbed62cef8782098468ef3da9d" ] ], - "timestamp": "2026-07-30T00:27:36.523004377", + "timestamp": "2026-07-30T19:01:15.217118703", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ngmaster/tests/main.nf.test.snap b/modules/ngmaster/tests/main.nf.test.snap index 7579c3c2c..9d6a72f1b 100644 --- a/modules/ngmaster/tests/main.nf.test.snap +++ b/modules/ngmaster/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-30T00:27:41.353453999", + "timestamp": "2026-07-30T19:01:14.868849062", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,510f19d76af81e52f423b70c5ea4a2b9" ] ], - "timestamp": "2026-07-30T00:28:04.721327371", + "timestamp": "2026-07-30T19:01:37.494870953", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/nohuman/run/tests/main.nf.test.snap b/modules/nohuman/run/tests/main.nf.test.snap index 4e91224cd..d28bde0da 100644 --- a/modules/nohuman/run/tests/main.nf.test.snap +++ b/modules/nohuman/run/tests/main.nf.test.snap @@ -19,7 +19,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-30T00:39:14.923721815", + "timestamp": "2026-07-30T19:13:22.75625609", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -45,7 +45,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-30T00:43:19.706825284", + "timestamp": "2026-07-30T19:17:55.590466404", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -71,7 +71,7 @@ "versions.yml:md5,795cd80ef4d2109d4aeadeaf8a025ad3" ] ], - "timestamp": "2026-07-30T00:34:26.778722457", + "timestamp": "2026-07-30T19:08:32.867396089", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/panaroo/run/tests/main.nf.test.snap b/modules/panaroo/run/tests/main.nf.test.snap index 00ac91f03..1e363902b 100644 --- a/modules/panaroo/run/tests/main.nf.test.snap +++ b/modules/panaroo/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,e6a0f1e191dcfb92fab2a7d68063c31d" ] ], - "timestamp": "2026-07-30T00:29:25.379571834", + "timestamp": "2026-07-30T19:02:53.705658675", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pasty/tests/main.nf.test.snap b/modules/pasty/tests/main.nf.test.snap index 05020df86..2e82d9485 100644 --- a/modules/pasty/tests/main.nf.test.snap +++ b/modules/pasty/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_000006765.blastn.tsv:md5,dcaf63876416cd5c19d868cfbf446258" ], - "timestamp": "2026-07-30T00:27:38.829262086", + "timestamp": "2026-07-30T19:01:09.628892017", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pbptyper/tests/main.nf.test.snap b/modules/pbptyper/tests/main.nf.test.snap index 7ae892c65..c140e0e0c 100644 --- a/modules/pbptyper/tests/main.nf.test.snap +++ b/modules/pbptyper/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "GCF_001457635.tblastn.tsv:md5,ce2247715df7d40f2ada2fe27e6c3967" ], - "timestamp": "2026-07-30T00:28:15.874910363", + "timestamp": "2026-07-30T19:01:50.334593871", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/phispy/tests/main.nf.test.snap b/modules/phispy/tests/main.nf.test.snap index 1d5f2afd3..f9b4cadcb 100644 --- a/modules/phispy/tests/main.nf.test.snap +++ b/modules/phispy/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,97542c4eb1d90b2b0a0375c916b75dc5" ] ], - "timestamp": "2026-07-30T00:29:58.59773508", + "timestamp": "2026-07-30T19:03:31.453893248", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pirate/tests/main.nf.test.snap b/modules/pirate/tests/main.nf.test.snap index 8c2cb043a..459cf9a57 100644 --- a/modules/pirate/tests/main.nf.test.snap +++ b/modules/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,ce4d40e2b87e2e5cac6e755fcb0c023b" ] ], - "timestamp": "2026-07-30T00:30:44.697742266", + "timestamp": "2026-07-30T19:04:14.89152874", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/plasmidfinder/tests/main.nf.test.snap b/modules/plasmidfinder/tests/main.nf.test.snap index 04311d63f..7fe5c6d5d 100644 --- a/modules/plasmidfinder/tests/main.nf.test.snap +++ b/modules/plasmidfinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-30T00:29:08.915528222", + "timestamp": "2026-07-30T19:02:35.403125645", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,2de62652dc2eb6c95f17225e88da8d70" ] ], - "timestamp": "2026-07-30T00:29:29.478069468", + "timestamp": "2026-07-30T19:02:55.239172022", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/pneumocat/tests/main.nf.test.snap b/modules/pneumocat/tests/main.nf.test.snap index 3667c7d48..342593564 100644 --- a/modules/pneumocat/tests/main.nf.test.snap +++ b/modules/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf" ] ], - "timestamp": "2026-07-30T00:29:21.57152769", + "timestamp": "2026-07-30T19:02:49.657546906", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/prokka/tests/main.nf.test.snap b/modules/prokka/tests/main.nf.test.snap index b51ba1760..b131e1746 100644 --- a/modules/prokka/tests/main.nf.test.snap +++ b/modules/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-30T00:29:52.218047901", + "timestamp": "2026-07-30T19:03:22.96725672", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-30T00:30:22.356426243", + "timestamp": "2026-07-30T19:03:55.701297764", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,edc57afe4ba0c950e15415ed95f1ff83" ] ], - "timestamp": "2026-07-30T00:31:06.553215483", + "timestamp": "2026-07-30T19:04:41.090391416", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/quast/tests/main.nf.test.snap b/modules/quast/tests/main.nf.test.snap index db9f5c254..4a6cd2fac 100644 --- a/modules/quast/tests/main.nf.test.snap +++ b/modules/quast/tests/main.nf.test.snap @@ -11,7 +11,7 @@ }, "SRR2838702.tsv:md5,79fa78c69537697be5eee30f630833d7" ], - "timestamp": "2026-07-30T00:30:03.390878259", + "timestamp": "2026-07-30T19:03:36.110797121", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -29,7 +29,7 @@ }, "SRR2838702.tsv:md5,a02f798379d9982810a198ec9b389079" ], - "timestamp": "2026-07-30T00:29:44.261319001", + "timestamp": "2026-07-30T19:03:16.886391528", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -47,7 +47,7 @@ }, "SRR2838702.tsv:md5,2e31a6f1283ca3a7aa253ab81266b85f" ], - "timestamp": "2026-07-30T00:29:21.397650785", + "timestamp": "2026-07-30T19:02:54.643753786", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/heatmap/tests/main.nf.test.snap b/modules/rgi/heatmap/tests/main.nf.test.snap index 222be3b27..1e55b183d 100644 --- a/modules/rgi/heatmap/tests/main.nf.test.snap +++ b/modules/rgi/heatmap/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,85fd687a901fef3c05e188fe49391c68" ] ], - "timestamp": "2026-07-30T00:29:26.318079261", + "timestamp": "2026-07-30T19:02:57.820482255", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/rgi/main/tests/main.nf.test.snap b/modules/rgi/main/tests/main.nf.test.snap index 12bbdba04..8911831bb 100644 --- a/modules/rgi/main/tests/main.nf.test.snap +++ b/modules/rgi/main/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-30T00:30:22.913079927", + "timestamp": "2026-07-30T19:03:51.30412458", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-30T00:32:54.333765302", + "timestamp": "2026-07-30T19:06:21.639037039", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,05dc31bdfb77fca95ad95c899ac55679" ] ], - "timestamp": "2026-07-30T00:31:37.128227456", + "timestamp": "2026-07-30T19:05:05.837709411", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/roary/tests/main.nf.test.snap b/modules/roary/tests/main.nf.test.snap index 17d158bda..0207b1540 100644 --- a/modules/roary/tests/main.nf.test.snap +++ b/modules/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,80c99c1b38b33ebcb7925eabba7ca2eb" ] ], - "timestamp": "2026-07-30T00:30:49.42146625", + "timestamp": "2026-07-30T19:04:20.772233767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sccmec/tests/main.nf.test.snap b/modules/sccmec/tests/main.nf.test.snap index 24c32376d..2f7af20c3 100644 --- a/modules/sccmec/tests/main.nf.test.snap +++ b/modules/sccmec/tests/main.nf.test.snap @@ -12,7 +12,7 @@ "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-30T00:29:24.986631049", + "timestamp": "2026-07-30T19:02:57.064252528", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -31,7 +31,7 @@ "GCF_000017085.targets.blastn.tsv:md5,5cd7054ed50c7d360feac0e51db54ac6", "GCF_000017085.regions.blastn.tsv:md5,ca426de41052a9f0bdcfb538610e5aa6" ], - "timestamp": "2026-07-30T00:29:43.649817563", + "timestamp": "2026-07-30T19:03:14.979579813", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/scoary/tests/main.nf.test.snap b/modules/scoary/tests/main.nf.test.snap index 9f9471bed..e598be570 100644 --- a/modules/scoary/tests/main.nf.test.snap +++ b/modules/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,f8f8a2300f84de4e8184c9dd33579ccd" ] ], - "timestamp": "2026-07-30T00:29:22.425655254", + "timestamp": "2026-07-30T19:02:53.210307337", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seqsero2/tests/main.nf.test.snap b/modules/seqsero2/tests/main.nf.test.snap index 927eacf2f..117e1d560 100644 --- a/modules/seqsero2/tests/main.nf.test.snap +++ b/modules/seqsero2/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-30T00:29:37.098376092", + "timestamp": "2026-07-30T19:03:08.774122348", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,5eae062ed95e0fb2e1bd8d268e0e1cdf" ] ], - "timestamp": "2026-07-30T00:29:22.232803566", + "timestamp": "2026-07-30T19:02:54.875039583", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/seroba/run/tests/main.nf.test.snap b/modules/seroba/run/tests/main.nf.test.snap index d661a554d..a08c3d084 100644 --- a/modules/seroba/run/tests/main.nf.test.snap +++ b/modules/seroba/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,e485bb335ccae3f5e5f24f35690633d3" ] ], - "timestamp": "2026-07-30T00:29:55.428514816", + "timestamp": "2026-07-30T19:03:26.894145021", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigapass/tests/main.nf.test.snap b/modules/shigapass/tests/main.nf.test.snap index e0ed2daa6..8b6fa536a 100644 --- a/modules/shigapass/tests/main.nf.test.snap +++ b/modules/shigapass/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-30T00:29:48.360417064", + "timestamp": "2026-07-30T19:03:29.660208062", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,dc87229b4755a3bb75942178c557e81f" ] ], - "timestamp": "2026-07-30T00:30:13.008214619", + "timestamp": "2026-07-30T19:03:55.808071331", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigatyper/tests/main.nf.test.snap b/modules/shigatyper/tests/main.nf.test.snap index 8c8d2e08f..d3ef0ee79 100644 --- a/modules/shigatyper/tests/main.nf.test.snap +++ b/modules/shigatyper/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,5546505c7719718340a0cd98ece587d8" ] ], - "timestamp": "2026-07-30T00:29:48.300878513", + "timestamp": "2026-07-30T19:03:21.41731488", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/shigeifinder/module.config b/modules/shigeifinder/module.config index 8018dc92f..4eedb72c0 100644 --- a/modules/shigeifinder/module.config +++ b/modules/shigeifinder/module.config @@ -14,7 +14,7 @@ process { ext.args = "" // Environment information - ext.toolName = "bioconda::shigeifinder=1.3.5".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::shigeifinder=1.3.5 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/shigeifinder:1.3.5--pyhdfd78af_0" ext.image = "https://depot.galaxyproject.org/singularity/shigeifinder:1.3.5--pyhdfd78af_0" ext.condaDir = "${params.condadir}" diff --git a/modules/shigeifinder/tests/main.nf.test.snap b/modules/shigeifinder/tests/main.nf.test.snap index a960599a7..9c27733ed 100644 --- a/modules/shigeifinder/tests/main.nf.test.snap +++ b/modules/shigeifinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-30T00:29:58.546208686", + "timestamp": "2026-07-30T19:03:30.769067653", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,3aa6f0d34a8c44bd11c7d989667bd6f1" ] ], - "timestamp": "2026-07-30T00:29:45.79707681", + "timestamp": "2026-07-30T19:03:17.614857836", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sistr/module.config b/modules/sistr/module.config index f33e3c34f..f03c1d101 100644 --- a/modules/sistr/module.config +++ b/modules/sistr/module.config @@ -17,7 +17,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::sistr_cmd=1.1.3".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::sistr_cmd=1.1.3 conda-forge::setuptools=80".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/sistr_cmd:1.1.3--pyhdc42f0e_2" ext.image = "https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.3--pyhdc42f0e_2" ext.condaDir = "${params.condadir}" diff --git a/modules/sistr/tests/main.nf.test.snap b/modules/sistr/tests/main.nf.test.snap index 08a03b13a..270afd6dc 100644 --- a/modules/sistr/tests/main.nf.test.snap +++ b/modules/sistr/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-30T00:30:16.287630692", + "timestamp": "2026-07-30T19:04:06.595709409", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,9cd2b041e26756435a56098355b5a2ca" ] ], - "timestamp": "2026-07-30T00:30:53.487750678", + "timestamp": "2026-07-30T19:04:43.68397046", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/core/tests/main.nf.test.snap b/modules/snippy/core/tests/main.nf.test.snap index 3b8ec10ca..9f93b5ee9 100644 --- a/modules/snippy/core/tests/main.nf.test.snap +++ b/modules/snippy/core/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,af05caa4daa181fbe9d7bf82d3383d93" ] ], - "timestamp": "2026-07-30T00:30:13.481417038", + "timestamp": "2026-07-30T19:03:50.222610599", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snippy/run/module.config b/modules/snippy/run/module.config index 018caec7e..a48ee2869 100644 --- a/modules/snippy/run/module.config +++ b/modules/snippy/run/module.config @@ -38,7 +38,7 @@ process { ].join(' ').replaceAll("\\s{2,}", " ").trim() // Environment information - ext.toolName = "bioconda::bactopia-variants=1.0.4".replace("=", "-").replace(":", "-").replace(" ", "-") + ext.toolName = "bioconda::bactopia-variants=1.0.4 bioconda::htslib=1.14".replace("=", "-").replace(":", "-").replace(" ", "-") ext.docker = "biocontainers/bactopia-variants:1.0.4--hdfd78af_0" ext.image = "https://depot.galaxyproject.org/singularity/bactopia-variants:1.0.4--hdfd78af_0" ext.condaDir = "${params.condadir}" diff --git a/modules/snippy/run/tests/main.nf.test.snap b/modules/snippy/run/tests/main.nf.test.snap index 00695be1b..e06490996 100644 --- a/modules/snippy/run/tests/main.nf.test.snap +++ b/modules/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-30T00:31:10.016003134", + "timestamp": "2026-07-30T19:04:49.535080607", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f9e5c81ae82caf719b7ce57287dad4f4" ] ], - "timestamp": "2026-07-30T00:30:37.245702654", + "timestamp": "2026-07-30T19:04:16.394330099", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/snpdists/tests/main.nf.test.snap b/modules/snpdists/tests/main.nf.test.snap index c74b7625b..d377a9876 100644 --- a/modules/snpdists/tests/main.nf.test.snap +++ b/modules/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,944b6ecf9bf11c38b608ae08b36d5e2d" ] ], - "timestamp": "2026-07-30T00:30:18.463312289", + "timestamp": "2026-07-30T19:03:50.180977938", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/spatyper/tests/main.nf.test.snap b/modules/spatyper/tests/main.nf.test.snap index 5dfa49ac5..94093fe3f 100644 --- a/modules/spatyper/tests/main.nf.test.snap +++ b/modules/spatyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-30T00:30:43.658738231", + "timestamp": "2026-07-30T19:04:15.484233021", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,07c621229eb9346a10efc0afe9d15e42" ] ], - "timestamp": "2026-07-30T00:30:26.055766212", + "timestamp": "2026-07-30T19:03:56.714025736", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap index 76f9c1e40..98b168f89 100644 --- a/modules/srahumanscrubber/scrub/tests/main.nf.test.snap +++ b/modules/srahumanscrubber/scrub/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-30T00:32:21.642160814", + "timestamp": "2026-07-30T19:05:52.828604552", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,78ab09ff9e54f2fbad4aa04b12b33c6d" ] ], - "timestamp": "2026-07-30T00:31:33.317790804", + "timestamp": "2026-07-30T19:05:01.738781786", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/ssuissero/tests/main.nf.test.snap b/modules/ssuissero/tests/main.nf.test.snap index 54612542c..93ae02492 100644 --- a/modules/ssuissero/tests/main.nf.test.snap +++ b/modules/ssuissero/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-30T00:30:25.226392647", + "timestamp": "2026-07-30T19:03:54.329996588", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757" ] ], - "timestamp": "2026-07-30T00:30:37.564989688", + "timestamp": "2026-07-30T19:04:06.814354767", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphopiasccmec/tests/main.nf.test.snap b/modules/staphopiasccmec/tests/main.nf.test.snap index 4a03e4a07..23b024fa0 100644 --- a/modules/staphopiasccmec/tests/main.nf.test.snap +++ b/modules/staphopiasccmec/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-30T00:30:27.458716495", + "timestamp": "2026-07-30T19:03:57.11173782", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,efa986cf837fac5b6e3bdd3dab8b424c" ] ], - "timestamp": "2026-07-30T00:30:40.137500387", + "timestamp": "2026-07-30T19:04:10.609380077", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/staphscan/tests/main.nf.test.snap b/modules/staphscan/tests/main.nf.test.snap index 58851d987..ad1ad6072 100644 --- a/modules/staphscan/tests/main.nf.test.snap +++ b/modules/staphscan/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,251f3e6b35be5f660d5fc8bc8456bde6" ] ], - "timestamp": "2026-07-30T00:30:43.880114172", + "timestamp": "2026-07-30T19:04:11.404109887", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stecfinder/tests/main.nf.test.snap b/modules/stecfinder/tests/main.nf.test.snap index afaac69ff..618b7eb2e 100644 --- a/modules/stecfinder/tests/main.nf.test.snap +++ b/modules/stecfinder/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-30T00:30:56.074503103", + "timestamp": "2026-07-31T13:21:56.221033981", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-30T00:30:44.761262358", + "timestamp": "2026-07-31T13:21:49.985962768", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1" ] ], - "timestamp": "2026-07-30T00:30:31.907468861", + "timestamp": "2026-07-31T13:21:42.832614002", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/stxtyper/tests/main.nf.test.snap b/modules/stxtyper/tests/main.nf.test.snap index 7129038d8..1c8e66b56 100644 --- a/modules/stxtyper/tests/main.nf.test.snap +++ b/modules/stxtyper/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f9ebd9c1f28e4ce3da541f707abeaa52" ] ], - "timestamp": "2026-07-30T00:30:40.993582478", + "timestamp": "2026-07-30T19:04:10.423071062", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/sylph/profile/tests/main.nf.test.snap b/modules/sylph/profile/tests/main.nf.test.snap index f9ba65670..af54fac7f 100644 --- a/modules/sylph/profile/tests/main.nf.test.snap +++ b/modules/sylph/profile/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-30T00:32:47.326426676", + "timestamp": "2026-07-30T19:06:21.556178856", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -37,7 +37,7 @@ "versions.yml:md5,375b8094ea3bcac7fbc91f023399030c" ] ], - "timestamp": "2026-07-30T00:31:38.283348181", + "timestamp": "2026-07-30T19:05:11.357725295", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/collate/tests/main.nf.test.snap b/modules/tbprofiler/collate/tests/main.nf.test.snap index e57985f5e..cd9504248 100644 --- a/modules/tbprofiler/collate/tests/main.nf.test.snap +++ b/modules/tbprofiler/collate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,3c3d5fbb783c5cb96c154683bf56699a" ] ], - "timestamp": "2026-07-30T00:31:01.086481659", + "timestamp": "2026-07-30T19:04:29.486545933", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/tbprofiler/profile/tests/main.nf.test.snap b/modules/tbprofiler/profile/tests/main.nf.test.snap index b0d5bf276..c790b2cf3 100644 --- a/modules/tbprofiler/profile/tests/main.nf.test.snap +++ b/modules/tbprofiler/profile/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-30T00:31:47.72057877", + "timestamp": "2026-07-30T19:05:14.950783052", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -35,7 +35,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-30T00:32:41.836741059", + "timestamp": "2026-07-30T19:06:09.887964917", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -56,7 +56,7 @@ "versions.yml:md5,f1c3cd99e94db777ec4d6163026785c3" ] ], - "timestamp": "2026-07-30T00:33:50.46224948", + "timestamp": "2026-07-30T19:07:17.00960342", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/modules/traitar/run/main.nf b/modules/traitar/run/main.nf index 50e27250d..d0611bdbd 100644 --- a/modules/traitar/run/main.nf +++ b/modules/traitar/run/main.nf @@ -74,20 +74,17 @@ process TRAITAR_RUN { process_name: task.ext.process_name ) - def is_compressed = fna.getName().endsWith(".gz") ? true : false - def fna_name = fna.getName().replace(".gz", "") + def is_compressed = fna.fileName.name.endsWith(".gz") ? true : false + def fna_name = fna.fileName.name.replace(".gz", "") """ - # Decompress input if needed + # Materialize a real (non-symlink) copy of the input inside the traitar input directory + mkdir -p input_dir if [ "${is_compressed}" == "true" ]; then - gzip -c -d ${fna} > ${fna_name} + gzip -c -d ${fna} > input_dir/${fna_name} else - cp -L ${fna} ${fna_name} + cp -L ${fna} input_dir/${fna_name} fi - # Create input directory and sample file for traitar - mkdir -p input_dir - mv ${fna_name} input_dir/ - cat > samples.tsv <<-SAMPLE_EOF sample_file_name\tsample_name ${fna_name}\t${prefix} diff --git a/modules/traitar/run/tests/main.nf.test.snap b/modules/traitar/run/tests/main.nf.test.snap index 9be570d56..14fdb2857 100644 --- a/modules/traitar/run/tests/main.nf.test.snap +++ b/modules/traitar/run/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-30T00:36:44.596384058", + "timestamp": "2026-07-30T19:10:34.745900564", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -33,7 +33,7 @@ "versions.yml:md5,54ab86ba7bfee8eefdc6e365ae52fa34" ] ], - "timestamp": "2026-07-30T00:42:30.217169799", + "timestamp": "2026-07-30T19:16:14.650770468", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/nextflow.config b/nextflow.config index c46bb15d3..0bb910de5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -122,7 +122,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/subworkflows/abricate/tests/main.nf.test.snap b/subworkflows/abricate/tests/main.nf.test.snap index b5749f58e..af3b46770 100644 --- a/subworkflows/abricate/tests/main.nf.test.snap +++ b/subworkflows/abricate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-07-30T00:31:30.423869908", + "timestamp": "2026-07-30T19:05:03.864721907", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/abritamr/tests/main.nf.test.snap b/subworkflows/abritamr/tests/main.nf.test.snap index 5d26353d8..0732b25cb 100644 --- a/subworkflows/abritamr/tests/main.nf.test.snap +++ b/subworkflows/abritamr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-07-30T00:35:37.041063985", + "timestamp": "2026-07-30T19:09:19.846381875", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/agrvate/tests/main.nf.test.snap b/subworkflows/agrvate/tests/main.nf.test.snap index 4da631644..58aba764e 100644 --- a/subworkflows/agrvate/tests/main.nf.test.snap +++ b/subworkflows/agrvate/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-30T00:31:33.007429645", + "timestamp": "2026-07-30T19:05:08.098446398", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/amrfinderplus/tests/main.nf.test.snap b/subworkflows/amrfinderplus/tests/main.nf.test.snap index c1a2e98ec..c4c96abf4 100644 --- a/subworkflows/amrfinderplus/tests/main.nf.test.snap +++ b/subworkflows/amrfinderplus/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-07-30T00:31:45.513803737", + "timestamp": "2026-07-30T19:05:14.825890533", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ariba/tests/main.nf.test.snap b/subworkflows/ariba/tests/main.nf.test.snap index 21b1b5403..543928172 100644 --- a/subworkflows/ariba/tests/main.nf.test.snap +++ b/subworkflows/ariba/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6" ] ], - "timestamp": "2026-07-30T00:38:28.71671844", + "timestamp": "2026-07-30T19:12:08.845212811", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap index d0f36818a..1a16de005 100644 --- a/subworkflows/bactopia/sketcher/tests/main.nf.test.snap +++ b/subworkflows/bactopia/sketcher/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e46de3078794860a978e2dd0b390c27c" ] ], - "timestamp": "2026-07-30T00:33:07.050007635", + "timestamp": "2026-07-30T19:06:43.855105932", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/bakta/tests/main.nf.test.snap b/subworkflows/bakta/tests/main.nf.test.snap index 5ad86605b..a3a75fa0f 100644 --- a/subworkflows/bakta/tests/main.nf.test.snap +++ b/subworkflows/bakta/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-30T00:35:58.969384589", + "timestamp": "2026-07-30T19:09:35.223715848", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastn/tests/main.nf.test.snap b/subworkflows/blastn/tests/main.nf.test.snap index a2deb8361..cc052fec3 100644 --- a/subworkflows/blastn/tests/main.nf.test.snap +++ b/subworkflows/blastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-30T00:32:05.903153684", + "timestamp": "2026-07-30T19:05:37.725284844", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastp/tests/main.nf.test.snap b/subworkflows/blastp/tests/main.nf.test.snap index 2d6d94aa1..662ad341b 100644 --- a/subworkflows/blastp/tests/main.nf.test.snap +++ b/subworkflows/blastp/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-30T00:32:07.283334472", + "timestamp": "2026-07-30T19:05:49.487214821", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/blastx/tests/main.nf.test.snap b/subworkflows/blastx/tests/main.nf.test.snap index 0a45e5237..6e89da84e 100644 --- a/subworkflows/blastx/tests/main.nf.test.snap +++ b/subworkflows/blastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-30T00:32:14.674402011", + "timestamp": "2026-07-30T19:05:58.487129005", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/btyper3/tests/main.nf.test.snap b/subworkflows/btyper3/tests/main.nf.test.snap index 351d1d225..53e24aa9a 100644 --- a/subworkflows/btyper3/tests/main.nf.test.snap +++ b/subworkflows/btyper3/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-07-30T00:34:08.956730486", + "timestamp": "2026-07-30T19:07:45.274792455", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/busco/tests/main.nf.test.snap b/subworkflows/busco/tests/main.nf.test.snap index a68ba71b3..4d240c8b9 100644 --- a/subworkflows/busco/tests/main.nf.test.snap +++ b/subworkflows/busco/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-07-30T00:32:53.545050122", + "timestamp": "2026-07-30T19:06:28.211435154", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm/tests/main.nf.test.snap b/subworkflows/checkm/tests/main.nf.test.snap index 1714a1af2..5f49137d1 100644 --- a/subworkflows/checkm/tests/main.nf.test.snap +++ b/subworkflows/checkm/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-07-30T00:34:40.244690509", + "timestamp": "2026-07-30T19:08:13.133953984", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/checkm2/tests/main.nf.test.snap b/subworkflows/checkm2/tests/main.nf.test.snap index 00c8214f7..bcac33b27 100644 --- a/subworkflows/checkm2/tests/main.nf.test.snap +++ b/subworkflows/checkm2/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-07-30T00:36:58.648228101", + "timestamp": "2026-07-30T19:10:36.485568906", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clermontyping/tests/main.nf.test.snap b/subworkflows/clermontyping/tests/main.nf.test.snap index 225cbc362..2c4be6e99 100644 --- a/subworkflows/clermontyping/tests/main.nf.test.snap +++ b/subworkflows/clermontyping/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-07-30T00:33:17.856793542", + "timestamp": "2026-07-30T19:06:55.148178691", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/clonalframeml/tests/main.nf.test.snap b/subworkflows/clonalframeml/tests/main.nf.test.snap index f3a052ef5..2ebd3f0ad 100644 --- a/subworkflows/clonalframeml/tests/main.nf.test.snap +++ b/subworkflows/clonalframeml/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,77f64a20eeab9152a61953ec5203b926" ] ], - "timestamp": "2026-07-30T00:34:05.952322455", + "timestamp": "2026-07-30T19:07:48.007411247", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/deacon/tests/main.nf.test.snap b/subworkflows/deacon/tests/main.nf.test.snap index 07077a745..ac424cc3a 100644 --- a/subworkflows/deacon/tests/main.nf.test.snap +++ b/subworkflows/deacon/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,9d3e1c1b5110e0048698861366ed5151" ] ], - "timestamp": "2026-07-30T00:33:19.720003517", + "timestamp": "2026-07-30T19:07:04.699052478", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/defensefinder/tests/main.nf.test.snap b/subworkflows/defensefinder/tests/main.nf.test.snap index 98bf38c5f..88919e36d 100644 --- a/subworkflows/defensefinder/tests/main.nf.test.snap +++ b/subworkflows/defensefinder/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,cac1e24b64c152890e712ac2077fc111" ] ], - "timestamp": "2026-07-30T00:34:00.925711291", + "timestamp": "2026-07-30T19:07:26.270786073", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ectyper/tests/main.nf.test.snap b/subworkflows/ectyper/tests/main.nf.test.snap index 41d710094..9efe8dfc4 100644 --- a/subworkflows/ectyper/tests/main.nf.test.snap +++ b/subworkflows/ectyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-30T00:33:39.573436078", + "timestamp": "2026-07-30T19:07:14.029195354", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/eggnog/tests/main.nf.test.snap b/subworkflows/eggnog/tests/main.nf.test.snap index 8a7df7b95..0b5ce71bc 100644 --- a/subworkflows/eggnog/tests/main.nf.test.snap +++ b/subworkflows/eggnog/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "scope": "sample" } ], - "timestamp": "2026-07-30T00:54:55.63046983", + "timestamp": "2026-07-30T19:22:52.015336258", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/emmtyper/tests/main.nf.test.snap b/subworkflows/emmtyper/tests/main.nf.test.snap index 1fd058f77..6f8c10824 100644 --- a/subworkflows/emmtyper/tests/main.nf.test.snap +++ b/subworkflows/emmtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-30T00:33:20.599767449", + "timestamp": "2026-07-30T19:07:04.056726262", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/fastani/tests/main.nf.test.snap b/subworkflows/fastani/tests/main.nf.test.snap index bf1698868..b97ca1883 100644 --- a/subworkflows/fastani/tests/main.nf.test.snap +++ b/subworkflows/fastani/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-30T00:33:23.274314219", + "timestamp": "2026-07-30T19:07:09.027992467", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gamma/tests/main.nf.test.snap b/subworkflows/gamma/tests/main.nf.test.snap index fe5d6b695..099595eb6 100644 --- a/subworkflows/gamma/tests/main.nf.test.snap +++ b/subworkflows/gamma/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-07-30T00:33:40.984944802", + "timestamp": "2026-07-30T19:07:17.199659091", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genomedl/tests/main.nf.test.snap b/subworkflows/genomedl/tests/main.nf.test.snap index cf44cb71e..95561ccd1 100644 --- a/subworkflows/genomedl/tests/main.nf.test.snap +++ b/subworkflows/genomedl/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-30T00:33:56.13524619", + "timestamp": "2026-07-30T19:07:30.869572426", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -39,7 +39,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-30T00:34:09.299195954", + "timestamp": "2026-07-30T19:07:46.945271158", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -62,7 +62,7 @@ "versions.yml:md5,df087e43d695dee0f2bfffa1d15991e8" ] ], - "timestamp": "2026-07-30T00:33:42.265850529", + "timestamp": "2026-07-30T19:07:17.057077214", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/genotyphi/tests/main.nf.test.snap b/subworkflows/genotyphi/tests/main.nf.test.snap index c478e6c1e..840cb8a68 100644 --- a/subworkflows/genotyphi/tests/main.nf.test.snap +++ b/subworkflows/genotyphi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-07-30T00:34:00.410523002", + "timestamp": "2026-07-30T19:07:34.831040245", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gigatyper/tests/main.nf.test.snap b/subworkflows/gigatyper/tests/main.nf.test.snap index be3962e14..ad69e237e 100644 --- a/subworkflows/gigatyper/tests/main.nf.test.snap +++ b/subworkflows/gigatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-30T00:34:06.395619732", + "timestamp": "2026-07-30T19:07:45.380812777", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gtdb/tests/main.nf.test.snap b/subworkflows/gtdb/tests/main.nf.test.snap index b33ee9ab3..d2791f09c 100644 --- a/subworkflows/gtdb/tests/main.nf.test.snap +++ b/subworkflows/gtdb/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-30T00:38:51.017195314", + "timestamp": "2026-07-30T19:12:33.027397678", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/gubbins/tests/main.nf.test.snap b/subworkflows/gubbins/tests/main.nf.test.snap index b8bd44314..02178e7b4 100644 --- a/subworkflows/gubbins/tests/main.nf.test.snap +++ b/subworkflows/gubbins/tests/main.nf.test.snap @@ -23,7 +23,7 @@ "versions.yml:md5,a8d93e0d6a006b32c088567301fe66c4" ] ], - "timestamp": "2026-07-30T00:34:44.058417638", + "timestamp": "2026-07-30T19:08:21.377346175", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hicap/tests/main.nf.test.snap b/subworkflows/hicap/tests/main.nf.test.snap index 333f39254..2e827487a 100644 --- a/subworkflows/hicap/tests/main.nf.test.snap +++ b/subworkflows/hicap/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-30T00:34:25.138723306", + "timestamp": "2026-07-30T19:08:09.508478543", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/hpsuissero/tests/main.nf.test.snap b/subworkflows/hpsuissero/tests/main.nf.test.snap index 92460192c..a3a45c73c 100644 --- a/subworkflows/hpsuissero/tests/main.nf.test.snap +++ b/subworkflows/hpsuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-30T00:34:19.520796177", + "timestamp": "2026-07-30T19:07:59.700450636", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/iqtree/tests/main.nf.test.snap b/subworkflows/iqtree/tests/main.nf.test.snap index 77df8b94e..21bfe90d3 100644 --- a/subworkflows/iqtree/tests/main.nf.test.snap +++ b/subworkflows/iqtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,35bdf120a286dc0efcc97ccb06895c0f" ] ], - "timestamp": "2026-07-30T00:34:29.238796807", + "timestamp": "2026-07-30T19:08:11.780210852", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ismapper/tests/main.nf.test.snap b/subworkflows/ismapper/tests/main.nf.test.snap index 68b798af7..298de654e 100644 --- a/subworkflows/ismapper/tests/main.nf.test.snap +++ b/subworkflows/ismapper/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-30T00:35:39.372749302", + "timestamp": "2026-07-30T19:09:31.040678879", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kleborate/tests/main.nf.test.snap b/subworkflows/kleborate/tests/main.nf.test.snap index f806ba64b..43f46df07 100644 --- a/subworkflows/kleborate/tests/main.nf.test.snap +++ b/subworkflows/kleborate/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-30T00:35:26.770609969", + "timestamp": "2026-07-30T19:09:15.449844749", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/kraken2/tests/main.nf.test.snap b/subworkflows/kraken2/tests/main.nf.test.snap index 69d88f093..481fc74d7 100644 --- a/subworkflows/kraken2/tests/main.nf.test.snap +++ b/subworkflows/kraken2/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-30T00:35:30.694078732", + "timestamp": "2026-07-30T19:09:32.267782138", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/legsta/tests/main.nf.test.snap b/subworkflows/legsta/tests/main.nf.test.snap index 9e9443a60..da7ecd81a 100644 --- a/subworkflows/legsta/tests/main.nf.test.snap +++ b/subworkflows/legsta/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-30T00:35:06.120555112", + "timestamp": "2026-07-30T19:09:04.379096665", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/lissero/tests/main.nf.test.snap b/subworkflows/lissero/tests/main.nf.test.snap index 3aa037bed..cc62737e9 100644 --- a/subworkflows/lissero/tests/main.nf.test.snap +++ b/subworkflows/lissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-30T00:35:10.201863302", + "timestamp": "2026-07-30T19:09:11.25598244", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashdist/tests/main.nf.test.snap b/subworkflows/mashdist/tests/main.nf.test.snap index e881118d1..322d68f38 100644 --- a/subworkflows/mashdist/tests/main.nf.test.snap +++ b/subworkflows/mashdist/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,fa387a5652585c181be4884eb12f37b0" ] ], - "timestamp": "2026-07-30T00:35:22.399281695", + "timestamp": "2026-07-30T19:09:35.313603632", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mashtree/tests/main.nf.test.snap b/subworkflows/mashtree/tests/main.nf.test.snap index d276b01b1..d34dbdf8a 100644 --- a/subworkflows/mashtree/tests/main.nf.test.snap +++ b/subworkflows/mashtree/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d8cd0c9b6f670d5ae21fda6592e85d32" ] ], - "timestamp": "2026-07-30T00:35:41.654238607", + "timestamp": "2026-07-30T19:09:55.83613098", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mcroni/tests/main.nf.test.snap b/subworkflows/mcroni/tests/main.nf.test.snap index ab5340a98..06a83255e 100644 --- a/subworkflows/mcroni/tests/main.nf.test.snap +++ b/subworkflows/mcroni/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,6eecf339ecef6511e62beca33a4b3fc6" ] ], - "timestamp": "2026-07-30T00:36:00.175515475", + "timestamp": "2026-07-30T19:10:00.448865968", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/meningotype/tests/main.nf.test.snap b/subworkflows/meningotype/tests/main.nf.test.snap index 4541103bf..e52f6a130 100644 --- a/subworkflows/meningotype/tests/main.nf.test.snap +++ b/subworkflows/meningotype/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2210210917992673f792050a55c95b2e" ] ], - "timestamp": "2026-07-30T00:36:08.262517224", + "timestamp": "2026-07-30T19:10:02.368707231", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/merlindist/tests/main.nf.test.snap b/subworkflows/merlindist/tests/main.nf.test.snap index d8ffc0c94..3f9f68a99 100644 --- a/subworkflows/merlindist/tests/main.nf.test.snap +++ b/subworkflows/merlindist/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,a714676ea5e603813de6640079a3f847" ] ], - "timestamp": "2026-07-30T00:37:21.789483284", + "timestamp": "2026-07-30T19:11:35.428250317", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/midas/tests/main.nf.test.snap b/subworkflows/midas/tests/main.nf.test.snap index 1be7f32b5..f00954f5b 100644 --- a/subworkflows/midas/tests/main.nf.test.snap +++ b/subworkflows/midas/tests/main.nf.test.snap @@ -27,7 +27,7 @@ "versions.yml:md5,66c2179f6d22e371b66b5d12ec5b0af1" ] ], - "timestamp": "2026-07-30T00:43:18.74344166", + "timestamp": "2026-07-30T19:19:54.855510421", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mlst/tests/main.nf.test.snap b/subworkflows/mlst/tests/main.nf.test.snap index fb32b97c3..846746aeb 100644 --- a/subworkflows/mlst/tests/main.nf.test.snap +++ b/subworkflows/mlst/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,082ad51a2f3d2c0b3a158586edc08efc" ] ], - "timestamp": "2026-07-30T00:36:55.791299455", + "timestamp": "2026-07-30T19:10:37.070143123", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mobsuite/tests/main.nf.test.snap b/subworkflows/mobsuite/tests/main.nf.test.snap index f83424fb0..a736afb0f 100644 --- a/subworkflows/mobsuite/tests/main.nf.test.snap +++ b/subworkflows/mobsuite/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,e586a98fe29a48792ce661d2649ada18" ] ], - "timestamp": "2026-07-30T00:38:13.125714476", + "timestamp": "2026-07-30T19:11:47.082890937", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/mykrobe/tests/main.nf.test b/subworkflows/mykrobe/tests/main.nf.test index 626d6c675..89cddbc0d 100644 --- a/subworkflows/mykrobe/tests/main.nf.test +++ b/subworkflows/mykrobe/tests/main.nf.test @@ -33,14 +33,18 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.out.sample_outputs != null }, { assert workflow.out.run_outputs != null }, + // Reproducible outputs { assert snapshot( sample.meta, - sample.csv, - sample.json, sample.versions, run.meta, run.versions ).match() }, + // Non-reproducible outputs + { assert [ + sample.csv, + sample.json + ].every { path(it).exists() } }, { assert sample.results != null }, { assert run.csv != null }, { assert run.results != null } diff --git a/subworkflows/mykrobe/tests/main.nf.test.snap b/subworkflows/mykrobe/tests/main.nf.test.snap index 42e6fefa0..0c5a4dcd0 100644 --- a/subworkflows/mykrobe/tests/main.nf.test.snap +++ b/subworkflows/mykrobe/tests/main.nf.test.snap @@ -10,8 +10,6 @@ "scope": "sample", "single_end": false }, - "SRR2838702.csv:md5,a27c093fe0789e56a7100d16ae757766", - "SRR2838702.json:md5,c27fd2ccc9ffc107511fa83ef4920897", [ "versions.yml:md5,0bb4264d1e075a8c456f1cb32275d24e" ], @@ -27,7 +25,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-30T00:37:05.95887141", + "timestamp": "2026-07-30T19:10:55.57576539", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ngmaster/tests/main.nf.test.snap b/subworkflows/ngmaster/tests/main.nf.test.snap index b090900c9..ae147ca96 100644 --- a/subworkflows/ngmaster/tests/main.nf.test.snap +++ b/subworkflows/ngmaster/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,9dbc0e8b7902e955ec10c94c11074f06" ] ], - "timestamp": "2026-07-30T00:37:09.347207654", + "timestamp": "2026-07-30T19:10:56.782220351", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/nohuman/tests/main.nf.test.snap b/subworkflows/nohuman/tests/main.nf.test.snap index 62c19208b..a1eec105d 100644 --- a/subworkflows/nohuman/tests/main.nf.test.snap +++ b/subworkflows/nohuman/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,75d067d7ecc44ec6c90a321b8103c997" ] ], - "timestamp": "2026-07-30T00:41:41.432319795", + "timestamp": "2026-07-30T19:15:29.943725377", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/panaroo/tests/main.nf.test.snap b/subworkflows/panaroo/tests/main.nf.test.snap index 322357c5f..8f67e8061 100644 --- a/subworkflows/panaroo/tests/main.nf.test.snap +++ b/subworkflows/panaroo/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,0e38cb68a88a1a2911e751e9a8ffd648" ] ], - "timestamp": "2026-07-30T00:38:41.892273206", + "timestamp": "2026-07-30T19:12:37.415429867", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pangenome/tests/main.nf.test.snap b/subworkflows/pangenome/tests/main.nf.test.snap index 689ed8366..ac5f50a6d 100644 --- a/subworkflows/pangenome/tests/main.nf.test.snap +++ b/subworkflows/pangenome/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:38:43.444283472", + "timestamp": "2026-07-30T19:12:40.800419458", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pasty/tests/main.nf.test.snap b/subworkflows/pasty/tests/main.nf.test.snap index 3089a75cc..27e165302 100644 --- a/subworkflows/pasty/tests/main.nf.test.snap +++ b/subworkflows/pasty/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "versions.yml:md5,d806f451289eb221f11075799712603e" ] ], - "timestamp": "2026-07-30T00:37:14.000856853", + "timestamp": "2026-07-30T19:11:28.31262834", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pbptyper/tests/main.nf.test.snap b/subworkflows/pbptyper/tests/main.nf.test.snap index d1a17282e..921044cab 100644 --- a/subworkflows/pbptyper/tests/main.nf.test.snap +++ b/subworkflows/pbptyper/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "versions.yml:md5,f52169fdc42464f8ece8fcb1e5591a18" ] ], - "timestamp": "2026-07-30T00:37:57.287439735", + "timestamp": "2026-07-30T19:12:11.60428864", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/phispy/tests/main.nf.test.snap b/subworkflows/phispy/tests/main.nf.test.snap index 504cea567..44377db50 100644 --- a/subworkflows/phispy/tests/main.nf.test.snap +++ b/subworkflows/phispy/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-30T00:40:16.532246227", + "timestamp": "2026-07-30T19:13:56.210712488", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pirate/tests/main.nf.test.snap b/subworkflows/pirate/tests/main.nf.test.snap index 4e0ab3f47..67d1c9606 100644 --- a/subworkflows/pirate/tests/main.nf.test.snap +++ b/subworkflows/pirate/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,424257d69beae21355dee29eac16ca77" ] ], - "timestamp": "2026-07-30T00:40:47.427737664", + "timestamp": "2026-07-30T19:14:38.42119919", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/plasmidfinder/tests/main.nf.test.snap b/subworkflows/plasmidfinder/tests/main.nf.test.snap index 416162060..83504d858 100644 --- a/subworkflows/plasmidfinder/tests/main.nf.test.snap +++ b/subworkflows/plasmidfinder/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-30T00:38:15.852444954", + "timestamp": "2026-07-30T19:12:01.881148662", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/pneumocat/tests/main.nf.test.snap b/subworkflows/pneumocat/tests/main.nf.test.snap index 7c76ef31f..2c83ab2fd 100644 --- a/subworkflows/pneumocat/tests/main.nf.test.snap +++ b/subworkflows/pneumocat/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-30T00:38:39.180792292", + "timestamp": "2026-07-30T19:12:25.102986681", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/prokka/tests/main.nf.test.snap b/subworkflows/prokka/tests/main.nf.test.snap index 1bf2bbcf0..505bbb25d 100644 --- a/subworkflows/prokka/tests/main.nf.test.snap +++ b/subworkflows/prokka/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-30T00:38:38.122207605", + "timestamp": "2026-07-30T19:12:14.800317482", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/quast/tests/main.nf.test.snap b/subworkflows/quast/tests/main.nf.test.snap index 64539fb17..64d852785 100644 --- a/subworkflows/quast/tests/main.nf.test.snap +++ b/subworkflows/quast/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "versions.yml:md5,f6625779099decc901ee6311371b1230" ] ], - "timestamp": "2026-07-30T00:38:58.645483063", + "timestamp": "2026-07-30T19:12:21.738672492", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/rgi/tests/main.nf.test.snap b/subworkflows/rgi/tests/main.nf.test.snap index 2c0bf004d..5be6d52bd 100644 --- a/subworkflows/rgi/tests/main.nf.test.snap +++ b/subworkflows/rgi/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,c1294552ba205b057bd368875a4eac93" ] ], - "timestamp": "2026-07-30T00:40:03.980615536", + "timestamp": "2026-07-30T19:13:40.096773406", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/roary/tests/main.nf.test.snap b/subworkflows/roary/tests/main.nf.test.snap index 2110ba8f1..f77af90cd 100644 --- a/subworkflows/roary/tests/main.nf.test.snap +++ b/subworkflows/roary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,d5496a62b5ffe9e5af444bfc53221551" ] ], - "timestamp": "2026-07-30T00:40:19.847026733", + "timestamp": "2026-07-30T19:13:59.378067522", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sccmec/tests/main.nf.test.snap b/subworkflows/sccmec/tests/main.nf.test.snap index 440b95606..bacc45455 100644 --- a/subworkflows/sccmec/tests/main.nf.test.snap +++ b/subworkflows/sccmec/tests/main.nf.test.snap @@ -23,7 +23,7 @@ "versions.yml:md5,c6ede7b0533855a33c127cafa29de747" ] ], - "timestamp": "2026-07-30T00:39:10.813370359", + "timestamp": "2026-07-30T19:12:54.160041131", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scoary/tests/main.nf.test.snap b/subworkflows/scoary/tests/main.nf.test.snap index 5bc53a554..f4ac6ca3e 100644 --- a/subworkflows/scoary/tests/main.nf.test.snap +++ b/subworkflows/scoary/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,36d9b366d4941f258a248bf7a31aecc7" ] ], - "timestamp": "2026-07-30T00:39:07.465628311", + "timestamp": "2026-07-30T19:12:49.541013549", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/scrubber/tests/main.nf.test.snap b/subworkflows/scrubber/tests/main.nf.test.snap index bff4edfea..844812451 100644 --- a/subworkflows/scrubber/tests/main.nf.test.snap +++ b/subworkflows/scrubber/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-30T00:43:27.033020962", + "timestamp": "2026-07-30T19:17:27.153424719", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "versions.yml:md5,7c379989d6fecf5c9291326ac25be5e5" ] ], - "timestamp": "2026-07-30T00:44:00.513288867", + "timestamp": "2026-07-30T19:17:56.811494688", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seqsero2/tests/main.nf.test.snap b/subworkflows/seqsero2/tests/main.nf.test.snap index 8e72353bb..bfa647db6 100644 --- a/subworkflows/seqsero2/tests/main.nf.test.snap +++ b/subworkflows/seqsero2/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-30T00:39:14.222160389", + "timestamp": "2026-07-30T19:12:54.293196556", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/seroba/tests/main.nf.test.snap b/subworkflows/seroba/tests/main.nf.test.snap index a7e130ecd..2474e5607 100644 --- a/subworkflows/seroba/tests/main.nf.test.snap +++ b/subworkflows/seroba/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,4fd4f724e2f19016eff39a2b524a9007" ] ], - "timestamp": "2026-07-30T00:40:08.848418362", + "timestamp": "2026-07-30T19:13:54.522408867", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigapass/tests/main.nf.test.snap b/subworkflows/shigapass/tests/main.nf.test.snap index 4528645ba..27aaf0ae5 100644 --- a/subworkflows/shigapass/tests/main.nf.test.snap +++ b/subworkflows/shigapass/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,f481607e2b7526fd798b2375bb3cc9c4" ] ], - "timestamp": "2026-07-30T00:39:36.318062243", + "timestamp": "2026-07-30T19:13:15.113506712", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigatyper/tests/main.nf.test.snap b/subworkflows/shigatyper/tests/main.nf.test.snap index 36b612788..78ef9174f 100644 --- a/subworkflows/shigatyper/tests/main.nf.test.snap +++ b/subworkflows/shigatyper/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-07-30T00:39:30.71064618", + "timestamp": "2026-07-30T19:13:22.196281372", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/shigeifinder/tests/main.nf.test.snap b/subworkflows/shigeifinder/tests/main.nf.test.snap index dd16e40dd..6e0763a13 100644 --- a/subworkflows/shigeifinder/tests/main.nf.test.snap +++ b/subworkflows/shigeifinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,bb067649d1cb0b7cc78ced0baa36bf0e" ] ], - "timestamp": "2026-07-30T00:39:37.775646804", + "timestamp": "2026-07-30T19:13:28.074432021", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sistr/tests/main.nf.test.snap b/subworkflows/sistr/tests/main.nf.test.snap index 80e7030c1..5e8ccec03 100644 --- a/subworkflows/sistr/tests/main.nf.test.snap +++ b/subworkflows/sistr/tests/main.nf.test.snap @@ -24,7 +24,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-30T00:40:14.391016151", + "timestamp": "2026-07-30T19:13:53.704450358", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/core/tests/main.nf.test.snap b/subworkflows/snippy/core/tests/main.nf.test.snap index 388a99584..813d7cda2 100644 --- a/subworkflows/snippy/core/tests/main.nf.test.snap +++ b/subworkflows/snippy/core/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8705955ac30d91d4bcce3b0571be3147" ] ], - "timestamp": "2026-07-30T00:40:23.733781279", + "timestamp": "2026-07-30T19:13:58.134716292", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snippy/run/tests/main.nf.test.snap b/subworkflows/snippy/run/tests/main.nf.test.snap index 015629a14..51d63773b 100644 --- a/subworkflows/snippy/run/tests/main.nf.test.snap +++ b/subworkflows/snippy/run/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,3a20f15dd89e01a265cbbae4bacd7f30" ] ], - "timestamp": "2026-07-30T00:40:55.55304233", + "timestamp": "2026-07-30T19:14:26.280572044", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/snpdists/tests/main.nf.test.snap b/subworkflows/snpdists/tests/main.nf.test.snap index a670303c6..099e80537 100644 --- a/subworkflows/snpdists/tests/main.nf.test.snap +++ b/subworkflows/snpdists/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,b7c9ec6305cc1637c144c82ba20a94d6" ] ], - "timestamp": "2026-07-30T00:40:48.890416169", + "timestamp": "2026-07-30T19:13:55.920195882", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/spatyper/tests/main.nf.test.snap b/subworkflows/spatyper/tests/main.nf.test.snap index ab2a69d7c..2984f2d75 100644 --- a/subworkflows/spatyper/tests/main.nf.test.snap +++ b/subworkflows/spatyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,2be001b7db8743258dd915dfe57337f4" ] ], - "timestamp": "2026-07-30T00:40:59.792203588", + "timestamp": "2026-07-30T19:14:09.528299458", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/srahumanscrubber/tests/main.nf.test.snap b/subworkflows/srahumanscrubber/tests/main.nf.test.snap index e40c5ac65..3883e2f69 100644 --- a/subworkflows/srahumanscrubber/tests/main.nf.test.snap +++ b/subworkflows/srahumanscrubber/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "versions.yml:md5,ca8ec5702526f2d59b7e3c5068c1c400" ] ], - "timestamp": "2026-07-30T00:42:49.312195453", + "timestamp": "2026-07-30T19:16:09.070609573", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ssuissero/tests/main.nf.test.snap b/subworkflows/ssuissero/tests/main.nf.test.snap index 00fde3976..92ee4b54a 100644 --- a/subworkflows/ssuissero/tests/main.nf.test.snap +++ b/subworkflows/ssuissero/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,b273046b082dd70970b8f4e189aa5498" ] ], - "timestamp": "2026-07-30T00:41:09.156836132", + "timestamp": "2026-07-30T19:14:39.43459786", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphopiasccmec/tests/main.nf.test.snap b/subworkflows/staphopiasccmec/tests/main.nf.test.snap index 925fc21ac..70a78ed97 100644 --- a/subworkflows/staphopiasccmec/tests/main.nf.test.snap +++ b/subworkflows/staphopiasccmec/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,f59d6534316ffe1998c60f98b212d80f" ] ], - "timestamp": "2026-07-30T00:41:15.267714089", + "timestamp": "2026-07-30T19:14:41.33671548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/staphscan/tests/main.nf.test.snap b/subworkflows/staphscan/tests/main.nf.test.snap index 006ce5699..1ffe48e82 100644 --- a/subworkflows/staphscan/tests/main.nf.test.snap +++ b/subworkflows/staphscan/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3848bf66b301b2b06d040f81eaac7e9b" ] ], - "timestamp": "2026-07-30T00:41:32.589847961", + "timestamp": "2026-07-30T19:14:53.926203839", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stecfinder/tests/main.nf.test.snap b/subworkflows/stecfinder/tests/main.nf.test.snap index 893d5e3d7..202c52d51 100644 --- a/subworkflows/stecfinder/tests/main.nf.test.snap +++ b/subworkflows/stecfinder/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,a4e0bfe59670d712011a3dc00f3abeb5" ] ], - "timestamp": "2026-07-30T00:41:23.126852804", + "timestamp": "2026-07-31T13:21:44.075556482", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/stxtyper/tests/main.nf.test.snap b/subworkflows/stxtyper/tests/main.nf.test.snap index 9a51b7ecf..627b22eed 100644 --- a/subworkflows/stxtyper/tests/main.nf.test.snap +++ b/subworkflows/stxtyper/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,3eac79f1285e1d758e61e2f98bc6a78c" ] ], - "timestamp": "2026-07-30T00:41:29.62237883", + "timestamp": "2026-07-30T19:15:08.802639631", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/sylph/tests/main.nf.test.snap b/subworkflows/sylph/tests/main.nf.test.snap index 244474c21..75906bfbb 100644 --- a/subworkflows/sylph/tests/main.nf.test.snap +++ b/subworkflows/sylph/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "versions.yml:md5,2a85d1cd25d2a88c77d90030e05e17cf" ] ], - "timestamp": "2026-07-30T00:42:36.144854671", + "timestamp": "2026-07-30T19:16:19.889738558", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastn/tests/main.nf.test.snap b/subworkflows/tblastn/tests/main.nf.test.snap index 05644a628..30518cfb7 100644 --- a/subworkflows/tblastn/tests/main.nf.test.snap +++ b/subworkflows/tblastn/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,413650f494aaf14a524501ce6dc5c959" ] ], - "timestamp": "2026-07-30T00:41:29.658176168", + "timestamp": "2026-07-30T19:15:20.703520807", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tblastx/tests/main.nf.test.snap b/subworkflows/tblastx/tests/main.nf.test.snap index 7c2b5e271..bc384691c 100644 --- a/subworkflows/tblastx/tests/main.nf.test.snap +++ b/subworkflows/tblastx/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,8ebdf55bc992d797630ad6f81b6cbe3d" ] ], - "timestamp": "2026-07-30T00:41:30.924199078", + "timestamp": "2026-07-30T19:15:26.801611766", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/tbprofiler/tests/main.nf.test.snap b/subworkflows/tbprofiler/tests/main.nf.test.snap index 3d62d2a89..831b151c5 100644 --- a/subworkflows/tbprofiler/tests/main.nf.test.snap +++ b/subworkflows/tbprofiler/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-07-30T00:42:31.103452925", + "timestamp": "2026-07-30T19:16:24.652824615", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/teton/tests/main.nf.test.snap b/subworkflows/teton/tests/main.nf.test.snap index 10c43e0fb..88a1c8ce7 100644 --- a/subworkflows/teton/tests/main.nf.test.snap +++ b/subworkflows/teton/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "teton_reads": "SRR2838702_R1.scrubbed.fastq.gz,SRR2838702_R2.scrubbed.fastq.gz" } ], - "timestamp": "2026-07-30T00:49:55.974959825", + "timestamp": "2026-07-30T19:21:55.28532386", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/traitar/tests/main.nf.test.snap b/subworkflows/traitar/tests/main.nf.test.snap index e74f39b92..f1ae2ba2c 100644 --- a/subworkflows/traitar/tests/main.nf.test.snap +++ b/subworkflows/traitar/tests/main.nf.test.snap @@ -35,7 +35,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-30T00:47:50.554103931", + "timestamp": "2026-07-30T19:21:11.431373717", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 5e3c5bba7..7c09193aa 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -168,7 +168,7 @@ ] ], - "timestamp": "2026-07-30T00:57:50.422910256", + "timestamp": "2026-07-30T19:31:16.008311548", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -261,7 +261,7 @@ ] ], - "timestamp": "2026-07-30T01:21:53.7845979", + "timestamp": "2026-07-30T19:55:01.74615677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -451,7 +451,7 @@ ] ], - "timestamp": "2026-07-30T01:12:28.590070477", + "timestamp": "2026-07-30T19:45:20.929483058", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -642,7 +642,7 @@ ] ], - "timestamp": "2026-07-30T01:18:49.15407833", + "timestamp": "2026-07-30T19:51:41.483948316", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -718,7 +718,7 @@ ] ], - "timestamp": "2026-07-30T01:19:41.53560151", + "timestamp": "2026-07-30T19:52:35.190860588", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -905,7 +905,7 @@ "SRR2838702.png:md5,90cfbd53df590d7542498269d4dda97a" ] ], - "timestamp": "2026-07-30T00:54:24.486805427", + "timestamp": "2026-07-30T19:27:53.525188399", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -970,7 +970,7 @@ ] ], - "timestamp": "2026-07-30T01:22:33.178533182", + "timestamp": "2026-07-30T19:55:40.866556785", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1144,7 +1144,7 @@ ] ], - "timestamp": "2026-07-30T01:03:22.40108832", + "timestamp": "2026-07-30T19:36:11.058832397", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1328,7 +1328,7 @@ ] ], - "timestamp": "2026-07-30T00:48:20.406695303", + "timestamp": "2026-07-30T19:21:32.093797996", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/versions.yml b/versions.yml index 2823bbcd1..37b402698 100644 --- a/versions.yml +++ b/versions.yml @@ -1,2 +1,2 @@ bactopia: 4.1.0 -nf-bactopia: 2.1.6 +nf-bactopia: 2.1.7 diff --git a/workflows/bactopia-tools/abricate/nextflow.config b/workflows/bactopia-tools/abricate/nextflow.config index a7b1e3240..dc33d0cf0 100644 --- a/workflows/bactopia-tools/abricate/nextflow.config +++ b/workflows/bactopia-tools/abricate/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/abricate/tests/main.nf.test.snap b/workflows/bactopia-tools/abricate/tests/main.nf.test.snap index 28d624de5..f79f54ddd 100644 --- a/workflows/bactopia-tools/abricate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/abricate/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,c6b552151ca3a9ccc54d58594e65789b" ] ], - "timestamp": "2026-07-30T00:42:21.651520957", + "timestamp": "2026-07-30T19:16:03.786653869", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/abritamr/nextflow.config b/workflows/bactopia-tools/abritamr/nextflow.config index 32da58938..d3afa3a4b 100644 --- a/workflows/bactopia-tools/abritamr/nextflow.config +++ b/workflows/bactopia-tools/abritamr/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap index 20bd8293c..565176816 100644 --- a/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/abritamr/tests/main.nf.test.snap @@ -52,7 +52,7 @@ "versions.yml:md5,31f7f5153ed3b9aa6a6e432ec7939e0b" ] ], - "timestamp": "2026-07-30T00:43:32.280989483", + "timestamp": "2026-07-30T19:17:21.788788979", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/agrvate/nextflow.config b/workflows/bactopia-tools/agrvate/nextflow.config index 01cf5b7d1..6307a2434 100644 --- a/workflows/bactopia-tools/agrvate/nextflow.config +++ b/workflows/bactopia-tools/agrvate/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap index d69aa4313..183386bc9 100644 --- a/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/agrvate/tests/main.nf.test.snap @@ -49,7 +49,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-30T00:42:31.671869271", + "timestamp": "2026-07-30T19:16:17.269503309", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -105,7 +105,7 @@ "versions.yml:md5,bff857ba4a2070f0d89b811a8050494e" ] ], - "timestamp": "2026-07-30T00:42:58.072399483", + "timestamp": "2026-07-30T19:16:41.929272582", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/amrfinderplus/nextflow.config b/workflows/bactopia-tools/amrfinderplus/nextflow.config index 8c37aafab..82ea2ac95 100644 --- a/workflows/bactopia-tools/amrfinderplus/nextflow.config +++ b/workflows/bactopia-tools/amrfinderplus/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap b/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap index d6969e90f..f3648d40b 100644 --- a/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/amrfinderplus/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-07-30T00:43:06.485400977", + "timestamp": "2026-07-30T19:16:59.997651863", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,c18211bbb02304cba7b3e93cbcaa44c6" ] ], - "timestamp": "2026-07-30T00:42:38.963555032", + "timestamp": "2026-07-30T19:16:34.688081586", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ariba/nextflow.config b/workflows/bactopia-tools/ariba/nextflow.config index e3f09e7af..cb39d553b 100644 --- a/workflows/bactopia-tools/ariba/nextflow.config +++ b/workflows/bactopia-tools/ariba/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap index d234259fa..3b4e5ada0 100644 --- a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap @@ -65,7 +65,7 @@ "versions.yml:md5,1a4d97856cb563f9b6c84132cd60d481" ] ], - "timestamp": "2026-07-30T00:43:25.331188609", + "timestamp": "2026-07-30T19:16:56.885968394", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/bakta/nextflow.config b/workflows/bactopia-tools/bakta/nextflow.config index 862e39360..a8a5c73c3 100644 --- a/workflows/bactopia-tools/bakta/nextflow.config +++ b/workflows/bactopia-tools/bakta/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap index 202d9e282..6631e3832 100644 --- a/workflows/bactopia-tools/bakta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/bakta/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-30T00:49:05.47202251", + "timestamp": "2026-07-30T19:22:51.889397801", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -103,7 +103,7 @@ "versions.yml:md5,e8bb3b82f221298fc735072f579e992b" ] ], - "timestamp": "2026-07-30T00:45:20.127079247", + "timestamp": "2026-07-30T19:18:47.954805677", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastn/nextflow.config b/workflows/bactopia-tools/blastn/nextflow.config index 0d3a88e25..41686ab5e 100644 --- a/workflows/bactopia-tools/blastn/nextflow.config +++ b/workflows/bactopia-tools/blastn/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/blastn/tests/main.nf.test.snap b/workflows/bactopia-tools/blastn/tests/main.nf.test.snap index 8bc486424..4646cea8f 100644 --- a/workflows/bactopia-tools/blastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-30T00:43:28.064010988", + "timestamp": "2026-07-30T19:17:00.329804837", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-30T00:43:05.276288988", + "timestamp": "2026-07-30T19:16:41.669872794", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,83da7e0cc2656aa0959a8b41dc452417" ] ], - "timestamp": "2026-07-30T00:43:49.867466682", + "timestamp": "2026-07-30T19:17:18.680727326", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastp/nextflow.config b/workflows/bactopia-tools/blastp/nextflow.config index 2dda66065..5cf5e2337 100644 --- a/workflows/bactopia-tools/blastp/nextflow.config +++ b/workflows/bactopia-tools/blastp/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/blastp/tests/main.nf.test.snap b/workflows/bactopia-tools/blastp/tests/main.nf.test.snap index f6608f686..03b15a706 100644 --- a/workflows/bactopia-tools/blastp/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastp/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-30T00:43:10.282178482", + "timestamp": "2026-07-30T19:16:43.63776288", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-30T00:43:31.585567498", + "timestamp": "2026-07-30T19:17:07.057310122", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,f96b9474386d395c01c2be97c4c63fea" ] ], - "timestamp": "2026-07-30T00:43:53.411722433", + "timestamp": "2026-07-30T19:17:25.176574423", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/blastx/nextflow.config b/workflows/bactopia-tools/blastx/nextflow.config index 9d85f5bfa..c81fe3e3b 100644 --- a/workflows/bactopia-tools/blastx/nextflow.config +++ b/workflows/bactopia-tools/blastx/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/blastx/tests/main.nf.test.snap b/workflows/bactopia-tools/blastx/tests/main.nf.test.snap index c57ea40b0..0536ba612 100644 --- a/workflows/bactopia-tools/blastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/blastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-30T00:43:34.64030189", + "timestamp": "2026-07-30T19:17:07.552368311", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-30T00:43:57.122912991", + "timestamp": "2026-07-30T19:17:25.894415558", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,8634f578eba8a3c37f4edffd83aad444" ] ], - "timestamp": "2026-07-30T00:43:14.515641371", + "timestamp": "2026-07-30T19:16:46.787202051", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/bracken/nextflow.config b/workflows/bactopia-tools/bracken/nextflow.config index 5fa25fef7..26b97af9c 100644 --- a/workflows/bactopia-tools/bracken/nextflow.config +++ b/workflows/bactopia-tools/bracken/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/bracken/tests/main.nf.test.snap b/workflows/bactopia-tools/bracken/tests/main.nf.test.snap index 44cfdb326..48c236208 100644 --- a/workflows/bactopia-tools/bracken/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/bracken/tests/main.nf.test.snap @@ -60,7 +60,7 @@ "bracken-species-abundance.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9" ] ], - "timestamp": "2026-07-30T00:56:52.050983859", + "timestamp": "2026-07-30T19:30:27.996338535", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -127,7 +127,7 @@ "bracken-species-abundance.tsv:md5,9f9ef5bab54b3cb593886171a47ed7b9" ] ], - "timestamp": "2026-07-30T00:48:52.84431721", + "timestamp": "2026-07-30T19:21:50.924466611", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/btyper3/nextflow.config b/workflows/bactopia-tools/btyper3/nextflow.config index 8a402b347..b6538ab64 100644 --- a/workflows/bactopia-tools/btyper3/nextflow.config +++ b/workflows/bactopia-tools/btyper3/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap index 2379c281a..e66a14e02 100644 --- a/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/btyper3/tests/main.nf.test.snap @@ -66,7 +66,7 @@ "versions.yml:md5,40ee298a3f689113440883cada3337aa" ] ], - "timestamp": "2026-07-30T00:45:02.010229412", + "timestamp": "2026-07-30T19:18:45.598803657", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/busco/nextflow.config b/workflows/bactopia-tools/busco/nextflow.config index 8a1d2c277..a65d8f8df 100644 --- a/workflows/bactopia-tools/busco/nextflow.config +++ b/workflows/bactopia-tools/busco/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/busco/tests/main.nf.test.snap b/workflows/bactopia-tools/busco/tests/main.nf.test.snap index c46dd12bd..eefb75cab 100644 --- a/workflows/bactopia-tools/busco/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/busco/tests/main.nf.test.snap @@ -287,7 +287,7 @@ "versions.yml:md5,06546ad8c9dee85b74317666718ef698" ] ], - "timestamp": "2026-07-30T00:43:47.105302199", + "timestamp": "2026-07-30T19:17:30.444141942", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/checkm/nextflow.config b/workflows/bactopia-tools/checkm/nextflow.config index ae061002c..7573b945d 100644 --- a/workflows/bactopia-tools/checkm/nextflow.config +++ b/workflows/bactopia-tools/checkm/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/checkm/tests/main.nf.test.snap b/workflows/bactopia-tools/checkm/tests/main.nf.test.snap index 84a5fb924..12ba8dd7c 100644 --- a/workflows/bactopia-tools/checkm/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/checkm/tests/main.nf.test.snap @@ -91,7 +91,7 @@ "versions.yml:md5,9f9cdf7e89a396b859a6aec91820283a" ] ], - "timestamp": "2026-07-30T00:45:29.156268312", + "timestamp": "2026-07-30T19:18:56.636549921", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/checkm2/nextflow.config b/workflows/bactopia-tools/checkm2/nextflow.config index 0ab63dadb..f5234ef49 100644 --- a/workflows/bactopia-tools/checkm2/nextflow.config +++ b/workflows/bactopia-tools/checkm2/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap b/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap index 261d8b175..7ca495949 100644 --- a/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/checkm2/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,b7cf6dd33e2fefeb729064b0d46f2081" ] ], - "timestamp": "2026-07-30T00:47:34.29018248", + "timestamp": "2026-07-30T19:21:06.180579199", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/clermontyping/nextflow.config b/workflows/bactopia-tools/clermontyping/nextflow.config index 60b270af7..8ee64dfe9 100644 --- a/workflows/bactopia-tools/clermontyping/nextflow.config +++ b/workflows/bactopia-tools/clermontyping/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap index b747e5165..874e6b526 100644 --- a/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/clermontyping/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "versions.yml:md5,867a114cb8d26e2302391ce5a5a0a959" ] ], - "timestamp": "2026-07-30T00:44:01.962764273", + "timestamp": "2026-07-30T19:17:42.187409267", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/defensefinder/nextflow.config b/workflows/bactopia-tools/defensefinder/nextflow.config index 9369f434b..6e01dbd02 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow.config +++ b/workflows/bactopia-tools/defensefinder/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap index a5d3eb4ca..631f06668 100644 --- a/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/defensefinder/tests/main.nf.test.snap @@ -70,7 +70,7 @@ "versions.yml:md5,cb06109c537fb7ff30a68b0a1197889d" ] ], - "timestamp": "2026-07-30T00:44:02.302378039", + "timestamp": "2026-07-30T19:17:42.044716531", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ectyper/nextflow.config b/workflows/bactopia-tools/ectyper/nextflow.config index be929677a..d3fd46f88 100644 --- a/workflows/bactopia-tools/ectyper/nextflow.config +++ b/workflows/bactopia-tools/ectyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap index 7b8526da4..4e96b7470 100644 --- a/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ectyper/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,c8ed62b01b9e766b6ba10622c55a02e1" ] ], - "timestamp": "2026-07-30T00:44:04.175633039", + "timestamp": "2026-07-30T19:18:01.411582423", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/eggnog/nextflow.config b/workflows/bactopia-tools/eggnog/nextflow.config index 85d535e8b..0c95ec0b5 100644 --- a/workflows/bactopia-tools/eggnog/nextflow.config +++ b/workflows/bactopia-tools/eggnog/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap index 9889cf922..9719ceb92 100644 --- a/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/eggnog/tests/main.nf.test.snap @@ -29,7 +29,7 @@ ] ], - "timestamp": "2026-07-30T00:49:56.471588516", + "timestamp": "2026-07-30T19:23:16.719033924", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/emmtyper/nextflow.config b/workflows/bactopia-tools/emmtyper/nextflow.config index 3d569c6d6..58778b384 100644 --- a/workflows/bactopia-tools/emmtyper/nextflow.config +++ b/workflows/bactopia-tools/emmtyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap index f4fe544d0..b323e1de8 100644 --- a/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/emmtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-30T00:44:21.091331159", + "timestamp": "2026-07-30T19:18:09.689209426", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "versions.yml:md5,f181bc0c0ea82cc9859e47cd3254e8d4" ] ], - "timestamp": "2026-07-30T00:44:49.719035522", + "timestamp": "2026-07-30T19:18:34.087009671", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/fastani/nextflow.config b/workflows/bactopia-tools/fastani/nextflow.config index 65557a51f..a600caf11 100644 --- a/workflows/bactopia-tools/fastani/nextflow.config +++ b/workflows/bactopia-tools/fastani/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap index cc8d43964..1f922eb7c 100644 --- a/workflows/bactopia-tools/fastani/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/fastani/tests/main.nf.test.snap @@ -38,7 +38,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-30T00:45:28.68337363", + "timestamp": "2026-07-30T19:19:21.878600645", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -95,7 +95,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-30T00:44:58.55557384", + "timestamp": "2026-07-30T19:18:48.969197461", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "versions.yml:md5,ec1c87c7160d76617e82583ad5b7740d" ] ], - "timestamp": "2026-07-30T00:44:33.002004404", + "timestamp": "2026-07-30T19:18:27.253450906", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gamma/nextflow.config b/workflows/bactopia-tools/gamma/nextflow.config index 54571dae7..e0fe1bc9d 100644 --- a/workflows/bactopia-tools/gamma/nextflow.config +++ b/workflows/bactopia-tools/gamma/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap index adc3881f0..7b1afada8 100644 --- a/workflows/bactopia-tools/gamma/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gamma/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "versions.yml:md5,d05d2269217aebb5587ece87b0666cf1" ] ], - "timestamp": "2026-07-30T00:44:54.001806821", + "timestamp": "2026-07-30T19:18:38.623764757", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/genotyphi/nextflow.config b/workflows/bactopia-tools/genotyphi/nextflow.config index 765cf3f79..977096f2f 100644 --- a/workflows/bactopia-tools/genotyphi/nextflow.config +++ b/workflows/bactopia-tools/genotyphi/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/genotyphi/tests/.nftignore b/workflows/bactopia-tools/genotyphi/tests/.nftignore index 72a5fcb38..6f049d6da 100644 --- a/workflows/bactopia-tools/genotyphi/tests/.nftignore +++ b/workflows/bactopia-tools/genotyphi/tests/.nftignore @@ -1,3 +1,4 @@ **/*.{err,gz,html,log,pdf,stderr,stdout} **/nf.command.* bactopia-runs/**/nf-reports/*.{dot,html} +**/tools/genotyphi/*.{csv,json} diff --git a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap index 3e17b32eb..75686d50c 100644 --- a/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/genotyphi/tests/main.nf.test.snap @@ -48,8 +48,6 @@ "bactopia-runs/genotyphi/nf-reports/genotyphi-timeline.html" ], [ - "SRR2838702.csv:md5,643005849779eff11e0efe92802b08b7", - "SRR2838702.json:md5,11d0f10a53184817ebadd0dfaa90dee0", "SRR2838702.tsv:md5,57f85f8f41b2fb817f7693d07483d035", "versions.yml:md5,d8debae1bdcd6e4662223d9b812dd3d7", "versions.yml:md5,58cc026392506e5ec5266f0276d70c35", @@ -57,7 +55,7 @@ "versions.yml:md5,1e61ab9091b0ddd88b14c86fa3488bea" ] ], - "timestamp": "2026-07-30T00:45:11.483259503", + "timestamp": "2026-07-30T19:18:45.29927388", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gigatyper/nextflow.config b/workflows/bactopia-tools/gigatyper/nextflow.config index c7fc2b9a1..6decfe009 100644 --- a/workflows/bactopia-tools/gigatyper/nextflow.config +++ b/workflows/bactopia-tools/gigatyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap index 89f8979a5..0fc3d83e0 100644 --- a/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gigatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,59922891ac61f5298b927f8e43eb5ae6" ] ], - "timestamp": "2026-07-30T00:45:29.195653485", + "timestamp": "2026-07-30T19:18:53.943082596", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/gtdb/nextflow.config b/workflows/bactopia-tools/gtdb/nextflow.config index ca65b727c..aa2e983e0 100644 --- a/workflows/bactopia-tools/gtdb/nextflow.config +++ b/workflows/bactopia-tools/gtdb/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap index 68e023005..8e0059bab 100644 --- a/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/gtdb/tests/main.nf.test.snap @@ -47,7 +47,7 @@ "versions.yml:md5,ec94f157437c25058fdce9d4346342a2" ] ], - "timestamp": "2026-07-30T00:50:01.444745006", + "timestamp": "2026-07-30T19:23:50.216152542", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hicap/nextflow.config b/workflows/bactopia-tools/hicap/nextflow.config index c405c2646..16b04d730 100644 --- a/workflows/bactopia-tools/hicap/nextflow.config +++ b/workflows/bactopia-tools/hicap/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap index c7bce652b..1643e02e2 100644 --- a/workflows/bactopia-tools/hicap/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hicap/tests/main.nf.test.snap @@ -61,7 +61,7 @@ "versions.yml:md5,0c84033bcf201f320a96434ff2545e4a" ] ], - "timestamp": "2026-07-30T00:45:50.612267949", + "timestamp": "2026-07-30T19:20:30.066864512", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/hpsuissero/nextflow.config b/workflows/bactopia-tools/hpsuissero/nextflow.config index 001f157ae..69359427a 100644 --- a/workflows/bactopia-tools/hpsuissero/nextflow.config +++ b/workflows/bactopia-tools/hpsuissero/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap index 5822d1593..cdeaf80f5 100644 --- a/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/hpsuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f6953ae2271fe2a3415f7a5450e4f046" ] ], - "timestamp": "2026-07-30T00:45:45.528481711", + "timestamp": "2026-07-30T19:20:21.196535053", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ismapper/nextflow.config b/workflows/bactopia-tools/ismapper/nextflow.config index 69efa8446..c0188b7ae 100644 --- a/workflows/bactopia-tools/ismapper/nextflow.config +++ b/workflows/bactopia-tools/ismapper/nextflow.config @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap index 54d081595..86efd5ef9 100644 --- a/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ismapper/tests/main.nf.test.snap @@ -1068,7 +1068,7 @@ "versions.yml:md5,5c8653f3402a5a6792c554eea616f71c" ] ], - "timestamp": "2026-07-30T00:47:37.732911537", + "timestamp": "2026-07-30T19:21:11.372643235", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kleborate/nextflow.config b/workflows/bactopia-tools/kleborate/nextflow.config index 03cf8bdbf..56a71ada7 100644 --- a/workflows/bactopia-tools/kleborate/nextflow.config +++ b/workflows/bactopia-tools/kleborate/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap index a7c77b633..182ffc397 100644 --- a/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kleborate/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "versions.yml:md5,2351aac91e4aee5e9cfa2bd7a6a1bda0" ] ], - "timestamp": "2026-07-30T00:47:30.390911941", + "timestamp": "2026-07-30T19:21:27.104169078", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/kraken2/nextflow.config b/workflows/bactopia-tools/kraken2/nextflow.config index 04439a30c..404ec32f7 100644 --- a/workflows/bactopia-tools/kraken2/nextflow.config +++ b/workflows/bactopia-tools/kraken2/nextflow.config @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap index 8814fff7c..4ca13a251 100644 --- a/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/kraken2/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-30T00:52:55.969610984", + "timestamp": "2026-07-30T19:26:30.987425103", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -63,7 +63,7 @@ "versions.yml:md5,121005727d1dfbf01116529f9640d2c5" ] ], - "timestamp": "2026-07-30T00:53:44.4624829", + "timestamp": "2026-07-30T19:27:19.843386225", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/legsta/nextflow.config b/workflows/bactopia-tools/legsta/nextflow.config index 44b07df73..272dcccd5 100644 --- a/workflows/bactopia-tools/legsta/nextflow.config +++ b/workflows/bactopia-tools/legsta/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap index 43b666c63..507112c00 100644 --- a/workflows/bactopia-tools/legsta/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/legsta/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f5386e7ff032be488d34b8bb980ba73b" ] ], - "timestamp": "2026-07-30T00:47:37.823359316", + "timestamp": "2026-07-30T19:21:06.266878903", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/lissero/nextflow.config b/workflows/bactopia-tools/lissero/nextflow.config index 700af26e3..3894470d8 100644 --- a/workflows/bactopia-tools/lissero/nextflow.config +++ b/workflows/bactopia-tools/lissero/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap index b3b368c57..2fdb29125 100644 --- a/workflows/bactopia-tools/lissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/lissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,f3f10093536274480dfa04035ebfbca2" ] ], - "timestamp": "2026-07-30T00:47:44.621782457", + "timestamp": "2026-07-30T19:21:06.877994198", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashdist/nextflow.config b/workflows/bactopia-tools/mashdist/nextflow.config index 161a735fb..9d0df5c65 100644 --- a/workflows/bactopia-tools/mashdist/nextflow.config +++ b/workflows/bactopia-tools/mashdist/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap index 057e738ec..59836480c 100644 --- a/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashdist/tests/main.nf.test.snap @@ -43,7 +43,7 @@ "mashdist.tsv:md5,630500729ddf987a8f487cd409d0afce" ] ], - "timestamp": "2026-07-30T00:47:55.734051336", + "timestamp": "2026-07-30T19:21:17.345056885", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mashtree/nextflow.config b/workflows/bactopia-tools/mashtree/nextflow.config index b62814547..6e5ac1b48 100644 --- a/workflows/bactopia-tools/mashtree/nextflow.config +++ b/workflows/bactopia-tools/mashtree/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap index 1711f75c1..a65c5f44f 100644 --- a/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mashtree/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "mashtree.dnd:md5,2b2d08b0bf16e25717f5db0eca6eba6b" ] ], - "timestamp": "2026-07-30T00:47:56.939857226", + "timestamp": "2026-07-30T19:21:21.13656432", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -59,7 +59,7 @@ "mashtree.dnd:md5,02f89fd1a5f4a3a92df0b016061f67dd" ] ], - "timestamp": "2026-07-30T00:48:27.071126803", + "timestamp": "2026-07-30T19:21:43.844483588", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mcroni/nextflow.config b/workflows/bactopia-tools/mcroni/nextflow.config index 334d25af3..33f0fb199 100644 --- a/workflows/bactopia-tools/mcroni/nextflow.config +++ b/workflows/bactopia-tools/mcroni/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap index 3c49f2ca8..a2a424f3d 100644 --- a/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mcroni/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "mcroni.tsv:md5,c5459d2965dfafe22f173023d0c35610" ] ], - "timestamp": "2026-07-30T00:48:02.987215097", + "timestamp": "2026-07-30T19:21:27.637231686", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/meningotype/nextflow.config b/workflows/bactopia-tools/meningotype/nextflow.config index 1ffcfbe58..fb053fd27 100644 --- a/workflows/bactopia-tools/meningotype/nextflow.config +++ b/workflows/bactopia-tools/meningotype/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap index f4e8e7874..069d4f146 100644 --- a/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/meningotype/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "meningotype.tsv:md5,cdf1cbd9f28a9ce2138f072c6d0ab391" ] ], - "timestamp": "2026-07-30T00:48:06.017330495", + "timestamp": "2026-07-30T19:21:31.081823696", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/merlin/nextflow.config b/workflows/bactopia-tools/merlin/nextflow.config index a8acf679d..a38422120 100644 --- a/workflows/bactopia-tools/merlin/nextflow.config +++ b/workflows/bactopia-tools/merlin/nextflow.config @@ -114,7 +114,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap index 4ea1cc3e4..86664ab02 100644 --- a/workflows/bactopia-tools/merlin/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/merlin/tests/main.nf.test.snap @@ -386,7 +386,7 @@ ] ], - "timestamp": "2026-07-30T00:49:36.893153419", + "timestamp": "2026-07-30T19:23:02.97683", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -973,7 +973,7 @@ ] ], - "timestamp": "2026-07-30T00:51:53.879010331", + "timestamp": "2026-07-30T19:25:20.93874873", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/midas/nextflow.config b/workflows/bactopia-tools/midas/nextflow.config index 85006c2ab..28f8512bf 100644 --- a/workflows/bactopia-tools/midas/nextflow.config +++ b/workflows/bactopia-tools/midas/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/midas/tests/main.nf.test.snap b/workflows/bactopia-tools/midas/tests/main.nf.test.snap index d789382f1..7edd75629 100644 --- a/workflows/bactopia-tools/midas/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/midas/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-30T00:48:41.343249956", + "timestamp": "2026-07-30T19:22:09.173693414", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -99,7 +99,7 @@ "midas.tsv:md5,6078fbf9d5c44a56afeb7a42836b14d2" ] ], - "timestamp": "2026-07-30T00:49:23.034024271", + "timestamp": "2026-07-30T19:23:12.153650008", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mlst/nextflow.config b/workflows/bactopia-tools/mlst/nextflow.config index c2e7353c6..01e620377 100644 --- a/workflows/bactopia-tools/mlst/nextflow.config +++ b/workflows/bactopia-tools/mlst/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap index 4d8864f1f..73999fc88 100644 --- a/workflows/bactopia-tools/mlst/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mlst/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "mlst.tsv:md5,c2faf73735d4ebc6fb0d8f4b263eb5b6" ] ], - "timestamp": "2026-07-30T00:48:15.899678948", + "timestamp": "2026-07-30T19:21:36.849565541", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mobsuite/nextflow.config b/workflows/bactopia-tools/mobsuite/nextflow.config index f91c8d0a1..b88698c73 100644 --- a/workflows/bactopia-tools/mobsuite/nextflow.config +++ b/workflows/bactopia-tools/mobsuite/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap index 81bcc9b32..bd4acc0e9 100644 --- a/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mobsuite/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "mobsuite.tsv:md5,951dbd706ab78c4d00aa28735ab34e87" ] ], - "timestamp": "2026-07-30T00:48:44.483859763", + "timestamp": "2026-07-30T19:22:27.604332423", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/mykrobe/nextflow.config b/workflows/bactopia-tools/mykrobe/nextflow.config index 8564e5008..589210158 100644 --- a/workflows/bactopia-tools/mykrobe/nextflow.config +++ b/workflows/bactopia-tools/mykrobe/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap index b8de1a178..eea70d695 100644 --- a/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/mykrobe/tests/main.nf.test.snap @@ -41,7 +41,7 @@ "versions.yml:md5,b61c6df6bd9d4c4092a94b7ebb604057" ] ], - "timestamp": "2026-07-30T00:48:20.875202495", + "timestamp": "2026-07-30T19:21:57.914687216", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ngmaster/nextflow.config b/workflows/bactopia-tools/ngmaster/nextflow.config index 4de56a598..e554dd35b 100644 --- a/workflows/bactopia-tools/ngmaster/nextflow.config +++ b/workflows/bactopia-tools/ngmaster/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap index dece7a5f8..3cfe2a9cc 100644 --- a/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ngmaster/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ngmaster.tsv:md5,2be2b3dd6c45726d2a9d7f2540b34219" ] ], - "timestamp": "2026-07-30T00:48:35.79817481", + "timestamp": "2026-07-30T19:22:04.188476944", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pangenome/nextflow.config b/workflows/bactopia-tools/pangenome/nextflow.config index bc56107f3..d60ae1cc9 100644 --- a/workflows/bactopia-tools/pangenome/nextflow.config +++ b/workflows/bactopia-tools/pangenome/nextflow.config @@ -93,7 +93,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap index 1c2f55ab7..588e8b92b 100644 --- a/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pangenome/tests/main.nf.test.snap @@ -140,7 +140,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:57:18.524040932", + "timestamp": "2026-07-30T19:30:46.745126115", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -314,7 +314,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:54:30.123243986", + "timestamp": "2026-07-30T19:28:00.244067439", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -447,7 +447,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:56:01.463760918", + "timestamp": "2026-07-30T19:29:29.722801387", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -579,7 +579,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:49:59.982072905", + "timestamp": "2026-07-30T19:23:29.45636356", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -663,7 +663,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:51:11.913708352", + "timestamp": "2026-07-30T19:24:41.470997199", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -747,7 +747,7 @@ "versions.yml:md5,3d37a0edadfd11d1e7e95ff8201e7f2a" ] ], - "timestamp": "2026-07-30T00:52:45.306300316", + "timestamp": "2026-07-30T19:26:13.960498899", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pasty/nextflow.config b/workflows/bactopia-tools/pasty/nextflow.config index c0a65596c..b708c99ed 100644 --- a/workflows/bactopia-tools/pasty/nextflow.config +++ b/workflows/bactopia-tools/pasty/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap index a80784b69..925bedf64 100644 --- a/workflows/bactopia-tools/pasty/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pasty/tests/main.nf.test.snap @@ -41,7 +41,7 @@ ] ], - "timestamp": "2026-07-30T00:48:43.962318083", + "timestamp": "2026-07-30T19:22:21.221326281", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pbptyper/nextflow.config b/workflows/bactopia-tools/pbptyper/nextflow.config index 1cea8a4a3..b6c41d74d 100644 --- a/workflows/bactopia-tools/pbptyper/nextflow.config +++ b/workflows/bactopia-tools/pbptyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap index d6b220719..25b6e3fe2 100644 --- a/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pbptyper/tests/main.nf.test.snap @@ -40,7 +40,7 @@ ] ], - "timestamp": "2026-07-30T00:49:33.255684955", + "timestamp": "2026-07-30T19:23:01.607640403", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/phispy/nextflow.config b/workflows/bactopia-tools/phispy/nextflow.config index fdbb993f5..b3b120128 100644 --- a/workflows/bactopia-tools/phispy/nextflow.config +++ b/workflows/bactopia-tools/phispy/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap index f852c32fd..4b3c82a85 100644 --- a/workflows/bactopia-tools/phispy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/phispy/tests/main.nf.test.snap @@ -60,7 +60,7 @@ "versions.yml:md5,07d57bb6615d099e188c1aad39da5c83" ] ], - "timestamp": "2026-07-30T00:49:56.554959703", + "timestamp": "2026-07-30T19:23:16.760576618", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/plasmidfinder/nextflow.config b/workflows/bactopia-tools/plasmidfinder/nextflow.config index d9fac182a..10698dbff 100644 --- a/workflows/bactopia-tools/plasmidfinder/nextflow.config +++ b/workflows/bactopia-tools/plasmidfinder/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap index 39d294aee..50e5c6246 100644 --- a/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/plasmidfinder/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,4f95221cf6912e60932c0c0c6982fba5" ] ], - "timestamp": "2026-07-30T00:49:16.446450824", + "timestamp": "2026-07-30T19:22:40.743868219", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/pneumocat/nextflow.config b/workflows/bactopia-tools/pneumocat/nextflow.config index 41bfa3d3e..debdbe358 100644 --- a/workflows/bactopia-tools/pneumocat/nextflow.config +++ b/workflows/bactopia-tools/pneumocat/nextflow.config @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap index 22471381e..937ded31b 100644 --- a/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/pneumocat/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,4c8b3e01e7425c78f2849d2e585f9cec" ] ], - "timestamp": "2026-07-30T00:49:13.046931953", + "timestamp": "2026-07-30T19:22:33.509557861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/prokka/nextflow.config b/workflows/bactopia-tools/prokka/nextflow.config index 36d42cb5d..7d39d72d0 100644 --- a/workflows/bactopia-tools/prokka/nextflow.config +++ b/workflows/bactopia-tools/prokka/nextflow.config @@ -85,7 +85,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap index 759bdc8e4..32e787f9e 100644 --- a/workflows/bactopia-tools/prokka/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/prokka/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,27f053a0892518f8b0fb60e2100e922e" ] ], - "timestamp": "2026-07-30T00:49:19.08682362", + "timestamp": "2026-07-30T19:22:43.125463361", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/quast/nextflow.config b/workflows/bactopia-tools/quast/nextflow.config index 1d6d3526f..a9e6ba3dc 100644 --- a/workflows/bactopia-tools/quast/nextflow.config +++ b/workflows/bactopia-tools/quast/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/quast/tests/main.nf.test.snap b/workflows/bactopia-tools/quast/tests/main.nf.test.snap index 343920b14..78e86e492 100644 --- a/workflows/bactopia-tools/quast/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/quast/tests/main.nf.test.snap @@ -67,7 +67,7 @@ "quast.tsv:md5,a02f798379d9982810a198ec9b389079" ] ], - "timestamp": "2026-07-30T00:49:29.718406164", + "timestamp": "2026-07-30T19:22:43.506155874", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/rgi/nextflow.config b/workflows/bactopia-tools/rgi/nextflow.config index 8a5081e4d..dee100534 100644 --- a/workflows/bactopia-tools/rgi/nextflow.config +++ b/workflows/bactopia-tools/rgi/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap index baac6972c..8e1b99836 100644 --- a/workflows/bactopia-tools/rgi/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/rgi/tests/main.nf.test.snap @@ -76,7 +76,7 @@ "versions.yml:md5,69941ec700f55e09c1a930ed36f54b0c" ] ], - "timestamp": "2026-07-30T00:50:15.440279652", + "timestamp": "2026-07-30T19:23:26.943897293", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sccmec/nextflow.config b/workflows/bactopia-tools/sccmec/nextflow.config index 0bae60834..3b9627c82 100644 --- a/workflows/bactopia-tools/sccmec/nextflow.config +++ b/workflows/bactopia-tools/sccmec/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap index 1f35e7dd1..88cdd751a 100644 --- a/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sccmec/tests/main.nf.test.snap @@ -43,7 +43,7 @@ ] ], - "timestamp": "2026-07-30T00:50:28.566688238", + "timestamp": "2026-07-30T19:23:17.524535618", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -93,7 +93,7 @@ ] ], - "timestamp": "2026-07-30T00:50:01.429639754", + "timestamp": "2026-07-30T19:22:49.162193084", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/scrubber/nextflow.config b/workflows/bactopia-tools/scrubber/nextflow.config index 88c45dd7a..64078a305 100644 --- a/workflows/bactopia-tools/scrubber/nextflow.config +++ b/workflows/bactopia-tools/scrubber/nextflow.config @@ -91,7 +91,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap index 74f530e63..83d89f5a0 100644 --- a/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/scrubber/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "scrubber.tsv:md5,c0ea3dcaa020751d8647c95a13fd362d" ] ], - "timestamp": "2026-07-30T00:50:21.45880484", + "timestamp": "2026-07-30T19:23:48.233499431", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -96,7 +96,7 @@ "scrubber.tsv:md5,e957775ff85716621f5fdd536de5b417" ] ], - "timestamp": "2026-07-30T00:53:28.98919548", + "timestamp": "2026-07-30T19:27:11.241723372", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -147,7 +147,7 @@ "scrubber.tsv:md5,9554a4a6929bbfd485e28acd4a716772" ] ], - "timestamp": "2026-07-30T00:54:37.238847702", + "timestamp": "2026-07-30T19:28:01.819430781", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seqsero2/nextflow.config b/workflows/bactopia-tools/seqsero2/nextflow.config index 54af2cc47..43ad3d019 100644 --- a/workflows/bactopia-tools/seqsero2/nextflow.config +++ b/workflows/bactopia-tools/seqsero2/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap index baed5d133..d2a472090 100644 --- a/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seqsero2/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "versions.yml:md5,407bddfba34298df26d7fa5880a564e6" ] ], - "timestamp": "2026-07-30T00:50:05.226773952", + "timestamp": "2026-07-30T19:23:32.123704349", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/seroba/nextflow.config b/workflows/bactopia-tools/seroba/nextflow.config index 30d904d5c..948b8bf0f 100644 --- a/workflows/bactopia-tools/seroba/nextflow.config +++ b/workflows/bactopia-tools/seroba/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap index c04da941e..4dfc08975 100644 --- a/workflows/bactopia-tools/seroba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/seroba/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "seroba.tsv:md5,8c20690cc5ca0fd77228c830001e0b86" ] ], - "timestamp": "2026-07-30T00:50:40.633000005", + "timestamp": "2026-07-30T19:24:02.483467787", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigapass/nextflow.config b/workflows/bactopia-tools/shigapass/nextflow.config index 321107a3f..7d4f4748e 100644 --- a/workflows/bactopia-tools/shigapass/nextflow.config +++ b/workflows/bactopia-tools/shigapass/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap index 02a76f0cd..c42359949 100644 --- a/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigapass/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "shigapass.tsv:md5,9982dbc252423a0507b7c397f66164f2" ] ], - "timestamp": "2026-07-30T00:50:27.038048511", + "timestamp": "2026-07-30T19:23:56.416662829", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigatyper/nextflow.config b/workflows/bactopia-tools/shigatyper/nextflow.config index 8470666fe..a20909873 100644 --- a/workflows/bactopia-tools/shigatyper/nextflow.config +++ b/workflows/bactopia-tools/shigatyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap index 078cacf59..ecbd671cc 100644 --- a/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigatyper/tests/main.nf.test.snap @@ -77,7 +77,7 @@ "versions.yml:md5,c4954fe5c276fcd3b66857bacafa932e" ] ], - "timestamp": "2026-07-30T00:50:33.174366621", + "timestamp": "2026-07-30T19:24:01.048048983", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/shigeifinder/nextflow.config b/workflows/bactopia-tools/shigeifinder/nextflow.config index 1af978427..9b52ea583 100644 --- a/workflows/bactopia-tools/shigeifinder/nextflow.config +++ b/workflows/bactopia-tools/shigeifinder/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap index f01a4005c..ce19098b8 100644 --- a/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/shigeifinder/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "shigeifinder.tsv:md5,25be6cf1161e59d9a4eab8db8f9b9ebb" ] ], - "timestamp": "2026-07-30T00:50:33.947678579", + "timestamp": "2026-07-30T19:23:57.511939415", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sistr/nextflow.config b/workflows/bactopia-tools/sistr/nextflow.config index 26cf199a3..39e28c745 100644 --- a/workflows/bactopia-tools/sistr/nextflow.config +++ b/workflows/bactopia-tools/sistr/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap index e3d3d9444..b31c8e02b 100644 --- a/workflows/bactopia-tools/sistr/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sistr/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "versions.yml:md5,683c9c1a0fff623520a6d84e3a7d0210" ] ], - "timestamp": "2026-07-30T00:51:24.491283507", + "timestamp": "2026-07-30T19:24:22.423253284", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/snippy/nextflow.config b/workflows/bactopia-tools/snippy/nextflow.config index 4aef670ab..13b4b6d6a 100644 --- a/workflows/bactopia-tools/snippy/nextflow.config +++ b/workflows/bactopia-tools/snippy/nextflow.config @@ -90,7 +90,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap index f521735cc..54935852e 100644 --- a/workflows/bactopia-tools/snippy/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/snippy/tests/main.nf.test.snap @@ -305,7 +305,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:52:34.38763914", + "timestamp": "2026-07-30T19:25:45.414550549", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -617,7 +617,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:54:12.826260331", + "timestamp": "2026-07-30T19:27:22.553780701", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -917,7 +917,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:55:12.658283959", + "timestamp": "2026-07-30T19:28:23.366290504", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1197,7 +1197,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:57:19.470508235", + "timestamp": "2026-07-30T19:30:36.794451447", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1509,7 +1509,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:56:31.359136857", + "timestamp": "2026-07-30T19:29:48.613556313", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -1789,7 +1789,7 @@ "core-snp.distance.tsv:md5,035f4fc57bee2ee25160fe42ca8307d1" ] ], - "timestamp": "2026-07-30T00:58:14.952886169", + "timestamp": "2026-07-30T19:31:27.02187471", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/spatyper/nextflow.config b/workflows/bactopia-tools/spatyper/nextflow.config index fcb3ffe9a..46f55a58d 100644 --- a/workflows/bactopia-tools/spatyper/nextflow.config +++ b/workflows/bactopia-tools/spatyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap index 1d43ef752..0b3d62ad8 100644 --- a/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/spatyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-07-30T00:52:05.067821814", + "timestamp": "2026-07-30T19:25:03.228802035", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "spatyper.tsv:md5,6afe7a90c591e32107d86c0e81029f54" ] ], - "timestamp": "2026-07-30T00:51:38.76960526", + "timestamp": "2026-07-30T19:24:28.910423382", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ssuissero/nextflow.config b/workflows/bactopia-tools/ssuissero/nextflow.config index 878c6f928..87b86a7d9 100644 --- a/workflows/bactopia-tools/ssuissero/nextflow.config +++ b/workflows/bactopia-tools/ssuissero/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap index 46aea26cd..9555054c6 100644 --- a/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ssuissero/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "ssuissero.tsv:md5,b1312d3041a6543154be554d5ec3b0b9" ] ], - "timestamp": "2026-07-30T00:51:31.22268183", + "timestamp": "2026-07-30T19:24:42.693652595", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphscan/nextflow.config b/workflows/bactopia-tools/staphscan/nextflow.config index 2b89d97a2..092f6660e 100644 --- a/workflows/bactopia-tools/staphscan/nextflow.config +++ b/workflows/bactopia-tools/staphscan/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap index 66b957237..6ab64c845 100644 --- a/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphscan/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "staphscan.tsv:md5,f13bc8d8aba4cf0f801e04a8d6148e1e" ] ], - "timestamp": "2026-07-30T00:51:43.72374962", + "timestamp": "2026-07-30T19:25:01.709535343", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/staphtyper/nextflow.config b/workflows/bactopia-tools/staphtyper/nextflow.config index 0d698fde4..6956e197f 100644 --- a/workflows/bactopia-tools/staphtyper/nextflow.config +++ b/workflows/bactopia-tools/staphtyper/nextflow.config @@ -89,7 +89,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap index f398cb559..230e20ce8 100644 --- a/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/staphtyper/tests/main.nf.test.snap @@ -112,7 +112,7 @@ "GCF_000017085.fna-error-report.tab:md5,44907dcabe3ed848aa68e87c0c6d00b2" ] ], - "timestamp": "2026-07-30T00:51:40.872100114", + "timestamp": "2026-07-30T19:25:10.047316684", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stecfinder/nextflow.config b/workflows/bactopia-tools/stecfinder/nextflow.config index 2a5742948..a12e1f673 100644 --- a/workflows/bactopia-tools/stecfinder/nextflow.config +++ b/workflows/bactopia-tools/stecfinder/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap index 24e56f9cb..d6fc37acb 100644 --- a/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stecfinder/tests/main.nf.test.snap @@ -71,7 +71,7 @@ "versions.yml:md5,a4e0bfe59670d712011a3dc00f3abeb5" ] ], - "timestamp": "2026-07-30T00:51:35.593049875", + "timestamp": "2026-07-31T13:21:50.78570325", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/stxtyper/nextflow.config b/workflows/bactopia-tools/stxtyper/nextflow.config index acbefdc82..d28cbf713 100644 --- a/workflows/bactopia-tools/stxtyper/nextflow.config +++ b/workflows/bactopia-tools/stxtyper/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap index 8b66ec5f5..266ae55a4 100644 --- a/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/stxtyper/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "stxtyper.tsv:md5,99f9ffe60fe519d684ee7943641022d2" ] ], - "timestamp": "2026-07-30T00:51:38.769202833", + "timestamp": "2026-07-30T19:25:14.090480976", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/sylph/nextflow.config b/workflows/bactopia-tools/sylph/nextflow.config index 846ab8b00..b445d995b 100644 --- a/workflows/bactopia-tools/sylph/nextflow.config +++ b/workflows/bactopia-tools/sylph/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap index 5d0f09b84..98c389f50 100644 --- a/workflows/bactopia-tools/sylph/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/sylph/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "sylph.tsv:md5,beb99cbcea3c9c0a90329ae09ee957f3" ] ], - "timestamp": "2026-07-30T00:52:24.032040616", + "timestamp": "2026-07-30T19:26:17.904289519", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastn/nextflow.config b/workflows/bactopia-tools/tblastn/nextflow.config index 83a5a08dd..efab0090f 100644 --- a/workflows/bactopia-tools/tblastn/nextflow.config +++ b/workflows/bactopia-tools/tblastn/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap index 549dacf98..75b605370 100644 --- a/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastn/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-30T00:51:35.302322173", + "timestamp": "2026-07-30T19:25:33.382686646", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastn.tsv:md5,cc21dacd4745b135d856a1aa329df046" ] ], - "timestamp": "2026-07-30T00:51:57.439961888", + "timestamp": "2026-07-30T19:25:53.805519502", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tblastx/nextflow.config b/workflows/bactopia-tools/tblastx/nextflow.config index 25f625fcc..74ce46b1e 100644 --- a/workflows/bactopia-tools/tblastx/nextflow.config +++ b/workflows/bactopia-tools/tblastx/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap index 0dd6cdbe7..3c570ac20 100644 --- a/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tblastx/tests/main.nf.test.snap @@ -42,7 +42,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-30T00:51:36.274913894", + "timestamp": "2026-07-30T19:25:37.144778827", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -91,7 +91,7 @@ "tblastx.tsv:md5,d3b6312d358a7fdb489d347094710033" ] ], - "timestamp": "2026-07-30T00:52:19.45682325", + "timestamp": "2026-07-30T19:26:20.76983511", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -140,7 +140,7 @@ "tblastx.tsv:md5,4efa1d2d8633246603e06df64e559c4c" ] ], - "timestamp": "2026-07-30T00:51:56.001229892", + "timestamp": "2026-07-30T19:25:58.297393537", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/tbprofiler/nextflow.config b/workflows/bactopia-tools/tbprofiler/nextflow.config index 906ca4513..97e3c3f70 100644 --- a/workflows/bactopia-tools/tbprofiler/nextflow.config +++ b/workflows/bactopia-tools/tbprofiler/nextflow.config @@ -86,7 +86,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap index 86bc826c4..6229629f1 100644 --- a/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/tbprofiler/tests/main.nf.test.snap @@ -48,7 +48,7 @@ "versions.yml:md5,d1d08404b1d56899be9ae1cf3c3aff3e" ] ], - "timestamp": "2026-07-30T00:52:30.057210326", + "timestamp": "2026-07-30T19:26:15.580362322", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/traitar/nextflow.config b/workflows/bactopia-tools/traitar/nextflow.config index 6f9be3887..9fae15613 100644 --- a/workflows/bactopia-tools/traitar/nextflow.config +++ b/workflows/bactopia-tools/traitar/nextflow.config @@ -87,7 +87,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap index 2a1b03913..550a8ed83 100644 --- a/workflows/bactopia-tools/traitar/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/traitar/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "versions.yml:md5,ec4bec02bbfd8002cdc3229b98111f6a" ] ], - "timestamp": "2026-07-30T00:56:35.787166831", + "timestamp": "2026-07-30T19:30:29.128552053", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/cleanyerreads/nextflow.config b/workflows/cleanyerreads/nextflow.config index 9ef6f6c84..0dace7024 100644 --- a/workflows/cleanyerreads/nextflow.config +++ b/workflows/cleanyerreads/nextflow.config @@ -95,7 +95,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/cleanyerreads/tests/main.nf.test.snap b/workflows/cleanyerreads/tests/main.nf.test.snap index 8ba4b8bbf..0d07e5442 100644 --- a/workflows/cleanyerreads/tests/main.nf.test.snap +++ b/workflows/cleanyerreads/tests/main.nf.test.snap @@ -83,7 +83,7 @@ ] ], - "timestamp": "2026-07-30T00:54:46.650311486", + "timestamp": "2026-07-30T19:28:21.446025394", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -157,7 +157,7 @@ ] ], - "timestamp": "2026-07-30T00:53:26.016521297", + "timestamp": "2026-07-30T19:26:54.451358248", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/staphopia/nextflow.config b/workflows/staphopia/nextflow.config index 3a934ad53..f2267c1ad 100644 --- a/workflows/staphopia/nextflow.config +++ b/workflows/staphopia/nextflow.config @@ -101,7 +101,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/staphopia/tests/main.nf.test.snap b/workflows/staphopia/tests/main.nf.test.snap index 8a07bde28..9e4560bbc 100644 --- a/workflows/staphopia/tests/main.nf.test.snap +++ b/workflows/staphopia/tests/main.nf.test.snap @@ -271,7 +271,7 @@ ] ], - "timestamp": "2026-07-30T00:57:24.825957304", + "timestamp": "2026-07-30T19:30:52.887024027", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/teton/nextflow.config b/workflows/teton/nextflow.config index 637952352..206f8f3c1 100644 --- a/workflows/teton/nextflow.config +++ b/workflows/teton/nextflow.config @@ -97,7 +97,7 @@ dag { // Plugins plugins { - id 'nf-bactopia@2.1.6' + id 'nf-bactopia@2.1.7' } bactopia { diff --git a/workflows/teton/tests/main.nf.test.snap b/workflows/teton/tests/main.nf.test.snap index 84bbea363..c8ded6650 100644 --- a/workflows/teton/tests/main.nf.test.snap +++ b/workflows/teton/tests/main.nf.test.snap @@ -169,7 +169,7 @@ ] ], - "timestamp": "2026-07-30T00:57:47.488165977", + "timestamp": "2026-07-30T19:31:47.758982804", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -344,7 +344,7 @@ ] ], - "timestamp": "2026-07-30T01:10:34.945146971", + "timestamp": "2026-07-30T19:43:51.415982337", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -519,7 +519,7 @@ ] ], - "timestamp": "2026-07-30T01:06:24.244779926", + "timestamp": "2026-07-30T19:40:13.1631072", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 99e374aa7b7b2d2ed442616ea8d2a9f2503648da Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 15:00:05 -0600 Subject: [PATCH 34/43] begin transition to generic context docs --- .../docs/project/01-repository-structure.md | 6 +- .../docs/project/02-development-workflow.md | 0 .../docs/project/03-configuration-system.md | 0 .../docs/project/04-testing-framework.md | 0 .../docs/reference/01-examples.md | 0 .../docs/reference/02-troubleshooting.md | 0 .../docs/reference/03-glossary.md | 0 .../docs/reference/04-plugin-functions.md | 0 .../docs/reference/05-task-ext-properties.md | 0 .../docs/reference/06-skills.md | 24 ++-- .../docs/standards/01-style-guide.md | 0 .../docs/standards/02-logic-rules.md | 0 .../docs/standards/03-technical-specs.md | 0 .../standards/04-subworkflow-documentation.md | 0 .../docs/standards/05-module-documentation.md | 0 .../standards/06-workflow-documentation.md | 0 .../docs/standards/07-tier-architecture.md | 0 .../skills/add-bactopia-tool/SKILL.md | 14 +- .../scripts/run-bactopia-lint.sh | 0 .../scripts/run-bactopia-scaffold.sh | 0 .../skills/add-module/SKILL.md | 14 +- .../skills/add-subworkflow/SKILL.md | 12 +- .../skills/bump-versions/SKILL.md | 6 +- .../skills/bump-versions/evals/evals.json | 0 .../bump-versions/scripts/bump_versions.py | 0 .../skills/merge-schemas/SKILL.md | 2 +- .../scripts/run-bactopia-merge-schemas.sh | 0 .../skills/project-status/SKILL.md | 2 +- .../scripts/run-bactopia-status.sh | 0 .../skills/release-checklist/SKILL.md | 18 +-- .../skills/release-checklist/evals/evals.json | 0 .../scripts/release_audit.py | 0 .../skills/review-citations/SKILL.md | 4 +- .../scripts/run-bactopia-citations.sh | 0 .../skills/review-docs/SKILL.md | 14 +- .../review-docs/scripts/run-bactopia-docs.sh | 0 .../skills/review-groovydoc/SKILL.md | 4 +- .../scripts/run-bactopia-lint.sh | 0 .../skills/review-tests/SKILL.md | 4 +- .../scripts/run-bactopia-review-tests.sh | 0 .../skills/run-tests/SKILL.md | 4 +- .../run-tests/scripts/run-bactopia-test.sh | 0 .../skills/update-catalog/SKILL.md | 2 +- .../scripts/run-bactopia-catalog.sh | 13 ++ .../skills/update-datasets/SKILL.md | 4 +- .../scripts/build-amrfinderplus-db.sh | 0 .../skills/update-module/SKILL.md | 2 +- .../scripts/run-bactopia-update.sh | 0 .claude/settings.json | 15 -- .claude/skills | 1 + .gitignore | 6 +- AGENTS.md | 131 +++++++++++++++++ CHANGELOG.md | 3 + CLAUDE.md | 132 +----------------- data/docs-patterns.yml | 2 +- llms.txt | 32 +++-- 56 files changed, 240 insertions(+), 231 deletions(-) rename {.claude => .agents}/docs/project/01-repository-structure.md (95%) rename {.claude => .agents}/docs/project/02-development-workflow.md (100%) rename {.claude => .agents}/docs/project/03-configuration-system.md (100%) rename {.claude => .agents}/docs/project/04-testing-framework.md (100%) rename {.claude => .agents}/docs/reference/01-examples.md (100%) rename {.claude => .agents}/docs/reference/02-troubleshooting.md (100%) rename {.claude => .agents}/docs/reference/03-glossary.md (100%) rename {.claude => .agents}/docs/reference/04-plugin-functions.md (100%) rename {.claude => .agents}/docs/reference/05-task-ext-properties.md (100%) rename {.claude => .agents}/docs/reference/06-skills.md (73%) rename {.claude => .agents}/docs/standards/01-style-guide.md (100%) rename {.claude => .agents}/docs/standards/02-logic-rules.md (100%) rename {.claude => .agents}/docs/standards/03-technical-specs.md (100%) rename {.claude => .agents}/docs/standards/04-subworkflow-documentation.md (100%) rename {.claude => .agents}/docs/standards/05-module-documentation.md (100%) rename {.claude => .agents}/docs/standards/06-workflow-documentation.md (100%) rename {.claude => .agents}/docs/standards/07-tier-architecture.md (100%) rename {.claude => .agents}/skills/add-bactopia-tool/SKILL.md (97%) rename {.claude => .agents}/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh (100%) rename {.claude => .agents}/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh (100%) rename {.claude => .agents}/skills/add-module/SKILL.md (96%) rename {.claude => .agents}/skills/add-subworkflow/SKILL.md (96%) rename {.claude => .agents}/skills/bump-versions/SKILL.md (96%) rename {.claude => .agents}/skills/bump-versions/evals/evals.json (100%) rename {.claude => .agents}/skills/bump-versions/scripts/bump_versions.py (100%) rename {.claude => .agents}/skills/merge-schemas/SKILL.md (98%) rename {.claude => .agents}/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh (100%) rename {.claude => .agents}/skills/project-status/SKILL.md (98%) rename {.claude => .agents}/skills/project-status/scripts/run-bactopia-status.sh (100%) rename {.claude => .agents}/skills/release-checklist/SKILL.md (97%) rename {.claude => .agents}/skills/release-checklist/evals/evals.json (100%) rename {.claude => .agents}/skills/release-checklist/scripts/release_audit.py (100%) rename {.claude => .agents}/skills/review-citations/SKILL.md (98%) rename {.claude => .agents}/skills/review-citations/scripts/run-bactopia-citations.sh (100%) rename {.claude => .agents}/skills/review-docs/SKILL.md (95%) rename {.claude => .agents}/skills/review-docs/scripts/run-bactopia-docs.sh (100%) rename {.claude => .agents}/skills/review-groovydoc/SKILL.md (98%) rename {.claude => .agents}/skills/review-groovydoc/scripts/run-bactopia-lint.sh (100%) rename {.claude => .agents}/skills/review-tests/SKILL.md (99%) rename {.claude => .agents}/skills/review-tests/scripts/run-bactopia-review-tests.sh (100%) rename {.claude => .agents}/skills/run-tests/SKILL.md (99%) rename {.claude => .agents}/skills/run-tests/scripts/run-bactopia-test.sh (100%) rename {.claude => .agents}/skills/update-catalog/SKILL.md (98%) rename {.claude => .agents}/skills/update-catalog/scripts/run-bactopia-catalog.sh (76%) rename {.claude => .agents}/skills/update-datasets/SKILL.md (97%) rename {.claude => .agents}/skills/update-datasets/scripts/build-amrfinderplus-db.sh (100%) rename {.claude => .agents}/skills/update-module/SKILL.md (98%) rename {.claude => .agents}/skills/update-module/scripts/run-bactopia-update.sh (100%) delete mode 100644 .claude/settings.json create mode 120000 .claude/skills create mode 100644 AGENTS.md diff --git a/.claude/docs/project/01-repository-structure.md b/.agents/docs/project/01-repository-structure.md similarity index 95% rename from .claude/docs/project/01-repository-structure.md rename to .agents/docs/project/01-repository-structure.md index 81b0eaacf..f159026be 100644 --- a/.claude/docs/project/01-repository-structure.md +++ b/.agents/docs/project/01-repository-structure.md @@ -7,7 +7,8 @@ The Bactopia repository follows a well-organized three-tier architecture that se ``` bactopia/ -├── .claude/ # AI context documentation (modular) +├── .agents/ # AI context: docs/ (modular documentation) and skills/ +├── .claude/ # Compatibility symlink: skills -> ../.agents/skills ├── .github/ # Github Actions workflows and issue templates ├── .vscode/ # Visual Studio Code settings and configurations ├── bin/ # Helper scripts and utilities @@ -26,7 +27,8 @@ bactopia/ ├── nextflow_schema.json # Parameter validation schema ├── catalog.json # Auto-generated component catalog ├── llms.txt # llms.txt-standard AI discovery index -├── CLAUDE.md # AI Context Master Map +├── AGENTS.md # AI Context Master Map (agents.md standard) +├── CLAUDE.md # One-line compatibility pointer importing AGENTS.md └── README.md # Project documentation ``` diff --git a/.claude/docs/project/02-development-workflow.md b/.agents/docs/project/02-development-workflow.md similarity index 100% rename from .claude/docs/project/02-development-workflow.md rename to .agents/docs/project/02-development-workflow.md diff --git a/.claude/docs/project/03-configuration-system.md b/.agents/docs/project/03-configuration-system.md similarity index 100% rename from .claude/docs/project/03-configuration-system.md rename to .agents/docs/project/03-configuration-system.md diff --git a/.claude/docs/project/04-testing-framework.md b/.agents/docs/project/04-testing-framework.md similarity index 100% rename from .claude/docs/project/04-testing-framework.md rename to .agents/docs/project/04-testing-framework.md diff --git a/.claude/docs/reference/01-examples.md b/.agents/docs/reference/01-examples.md similarity index 100% rename from .claude/docs/reference/01-examples.md rename to .agents/docs/reference/01-examples.md diff --git a/.claude/docs/reference/02-troubleshooting.md b/.agents/docs/reference/02-troubleshooting.md similarity index 100% rename from .claude/docs/reference/02-troubleshooting.md rename to .agents/docs/reference/02-troubleshooting.md diff --git a/.claude/docs/reference/03-glossary.md b/.agents/docs/reference/03-glossary.md similarity index 100% rename from .claude/docs/reference/03-glossary.md rename to .agents/docs/reference/03-glossary.md diff --git a/.claude/docs/reference/04-plugin-functions.md b/.agents/docs/reference/04-plugin-functions.md similarity index 100% rename from .claude/docs/reference/04-plugin-functions.md rename to .agents/docs/reference/04-plugin-functions.md diff --git a/.claude/docs/reference/05-task-ext-properties.md b/.agents/docs/reference/05-task-ext-properties.md similarity index 100% rename from .claude/docs/reference/05-task-ext-properties.md rename to .agents/docs/reference/05-task-ext-properties.md diff --git a/.claude/docs/reference/06-skills.md b/.agents/docs/reference/06-skills.md similarity index 73% rename from .claude/docs/reference/06-skills.md rename to .agents/docs/reference/06-skills.md index 702faee96..1f2afe75c 100644 --- a/.claude/docs/reference/06-skills.md +++ b/.agents/docs/reference/06-skills.md @@ -2,9 +2,9 @@ ## Overview -Skills are AI tooling — short instruction files that Claude invokes via the `Skill` tool when a matching trigger phrase appears. They are distinct from pipeline components (modules, subworkflows, workflows) and are **not** listed in [catalog.json](../../../catalog.json); this doc is the authoritative inventory for project-local skills. +Skills are AI tooling — short instruction files that the agent loads when a matching trigger phrase appears in its skill index. They are distinct from pipeline components (modules, subworkflows, workflows) and are **not** listed in [catalog.json](../../../catalog.json); this doc is the authoritative inventory for project-local skills. -**Pattern**: every project-local skill is a thin AI wrapper over a `bactopia-*` CLI in [bactopia-py](../../../../bactopia-py/bactopia/cli/). The skill lives at `.claude/skills//SKILL.md`; a wrapper script under `scripts/` discovers and invokes the CLI. Implementation logic belongs in the CLI so it can evolve independently and be run directly from the shell or CI — the `SKILL.md` is just interpretation. +**Pattern**: every project-local skill is a thin AI wrapper over a `bactopia-*` CLI in [bactopia-py](../../../../bactopia-py/bactopia/cli/). The skill lives at `.agents/skills//SKILL.md`; a wrapper script under `scripts/` discovers and invokes the CLI. Implementation logic belongs in the CLI so it can evolve independently and be run directly from the shell or CI — the `SKILL.md` is just interpretation. ## Project-local skills @@ -18,7 +18,7 @@ Skills are AI tooling — short instruction files that Claude invokes via the `S | [project-status](../../skills/project-status/) | `bactopia-status` | Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues. | | [release-checklist](../../skills/release-checklist/) | — | Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report. | | [review-citations](../../skills/review-citations/) | `bactopia-citations` | Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate. | -| [review-docs](../../skills/review-docs/) | `bactopia-docs` | Review staleness of reference docs under .claude/docs/ using bactopia-docs --validate. | +| [review-docs](../../skills/review-docs/) | `bactopia-docs` | Review staleness of reference docs under .agents/docs/ using bactopia-docs --validate. | | [review-groovydoc](../../skills/review-groovydoc/) | `bactopia-lint` | Review GroovyDoc accuracy across modules and subworkflows using bactopia-lint. | | [review-tests](../../skills/review-tests/) | — | Review nf-test run results and present a diagnostic summary with grouped error analysis. | | [run-tests](../../skills/run-tests/) | `bactopia-test` | Run Bactopia nf-tests via bactopia-test and produce a timestamped logs/ directory that /review-tests can interpret. | @@ -30,15 +30,13 @@ The `Purpose` column is the first sentence of each skill's `description:` frontm ## Global skills worth knowing -These live at `~/.claude/skills/` (user-global) or are built into the Claude Code harness: +These live at `~/.agents/skills/` (user-global, shared across harnesses) or are built into the agent harness: | Skill | When to use | |---|---| | `skill-creator` | **Any time** you are creating, editing, or improving a skill. Do not hand-scaffold `SKILL.md` files. | -| `session-handoff` | Save session context to the clipboard for resuming in a new session. | -| `update-config` | Configure the Claude Code harness via `settings.json` (hooks, permissions, status line). | -| `schedule` / `loop` | Recurring cron-style agents (`schedule`) or self-paced polling (`loop`). | -| `claude-api` | Reference for building apps on the Anthropic SDK — unrelated to the Bactopia pipeline. | + +Harnesses ship their own built-in skills on top of these (e.g. session handoff, config helpers) — consult your harness's skill list for those. ## When to invoke `skill-creator` @@ -54,7 +52,7 @@ Use it whenever the request is about *making* or *modifying* a skill: ## Architecture ```text -.claude/skills// +.agents/skills// SKILL.md # Frontmatter (name, description) + trigger instructions scripts/ # Optional — wrapper scripts run-bactopia-*.sh # Discovers the bactopia-* CLI in PATH or conda envs @@ -62,10 +60,10 @@ Use it whenever the request is about *making* or *modifying* a skill: Wrapper scripts find the backing CLI in this order: PATH first, then the exact bactopia-dev conda env, then exact bactopia-py, then any `bactopia-*` env (fuzzy match). This discovery code is shared across every wrapper, so env-setup changes propagate uniformly. -**Adding a new CLI-backed skill**: implement the CLI in [bactopia-py](../../../../bactopia-py/bactopia/cli/) first so it's testable, stable, and runnable outside Claude, then wrap it with `skill-creator`. The skill becomes the trigger surface; the CLI is the logic. +**Adding a new CLI-backed skill**: implement the CLI in [bactopia-py](../../../../bactopia-py/bactopia/cli/) first so it's testable, stable, and runnable outside an agent harness, then wrap it with `skill-creator`. The skill becomes the trigger surface; the CLI is the logic. ## Discoverability -- **Terminal CLI**: custom skills appear in the `/` autocomplete menu. -- **VS Code extension**: custom skills do **not** appear in the slash-command menu (known limitation). They still work — type `/skill-name` directly or describe what you want and Claude will trigger them via the same system reminder that enumerates skills at session start. -- This reference doc is linked from [CLAUDE.md](../../../CLAUDE.md) and [llms.txt](../../../llms.txt) so Claude has a canonical inventory to consult. +- **Slash commands**: most harnesses expose skills as `/skill:` (or list them in the `/` autocomplete menu). +- **Automatic triggering**: the harness enumerates skill names + descriptions at session start; the model loads the full `SKILL.md` when a description matches the task. Trigger phrases in `description:` are therefore the routing surface — keep them current. +- This reference doc is linked from [AGENTS.md](../../../AGENTS.md) and [llms.txt](../../../llms.txt) so agents have a canonical inventory to consult. diff --git a/.claude/docs/standards/01-style-guide.md b/.agents/docs/standards/01-style-guide.md similarity index 100% rename from .claude/docs/standards/01-style-guide.md rename to .agents/docs/standards/01-style-guide.md diff --git a/.claude/docs/standards/02-logic-rules.md b/.agents/docs/standards/02-logic-rules.md similarity index 100% rename from .claude/docs/standards/02-logic-rules.md rename to .agents/docs/standards/02-logic-rules.md diff --git a/.claude/docs/standards/03-technical-specs.md b/.agents/docs/standards/03-technical-specs.md similarity index 100% rename from .claude/docs/standards/03-technical-specs.md rename to .agents/docs/standards/03-technical-specs.md diff --git a/.claude/docs/standards/04-subworkflow-documentation.md b/.agents/docs/standards/04-subworkflow-documentation.md similarity index 100% rename from .claude/docs/standards/04-subworkflow-documentation.md rename to .agents/docs/standards/04-subworkflow-documentation.md diff --git a/.claude/docs/standards/05-module-documentation.md b/.agents/docs/standards/05-module-documentation.md similarity index 100% rename from .claude/docs/standards/05-module-documentation.md rename to .agents/docs/standards/05-module-documentation.md diff --git a/.claude/docs/standards/06-workflow-documentation.md b/.agents/docs/standards/06-workflow-documentation.md similarity index 100% rename from .claude/docs/standards/06-workflow-documentation.md rename to .agents/docs/standards/06-workflow-documentation.md diff --git a/.claude/docs/standards/07-tier-architecture.md b/.agents/docs/standards/07-tier-architecture.md similarity index 100% rename from .claude/docs/standards/07-tier-architecture.md rename to .agents/docs/standards/07-tier-architecture.md diff --git a/.claude/skills/add-bactopia-tool/SKILL.md b/.agents/skills/add-bactopia-tool/SKILL.md similarity index 97% rename from .claude/skills/add-bactopia-tool/SKILL.md rename to .agents/skills/add-bactopia-tool/SKILL.md index c953a6a90..a9dd6380b 100644 --- a/.claude/skills/add-bactopia-tool/SKILL.md +++ b/.agents/skills/add-bactopia-tool/SKILL.md @@ -24,8 +24,8 @@ This skill handles the **common single-tool pattern** which covers ~80% of bacto ## Prerequisites Before using this skill, read: -- `.claude/docs/standards/05-module-documentation.md` -- Module GroovyDoc standards -- `.claude/docs/standards/04-subworkflow-documentation.md` -- Subworkflow GroovyDoc standards +- `.agents/docs/standards/05-module-documentation.md` -- Module GroovyDoc standards +- `.agents/docs/standards/04-subworkflow-documentation.md` -- Subworkflow GroovyDoc standards ## Interactive Questioning @@ -50,7 +50,7 @@ Follow these phases in order. When unsure about ANYTHING, ask the user rather th 2. Run the lookup command: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty ``` 3. The output includes: @@ -115,7 +115,7 @@ with "(Recommended)" at the end of its label and place it first in the options l 3. **Run test-data discovery** based on the input type selected in Batch 1: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty ``` This returns species/accession combinations already used by similar modules, with pre-computed `test_data_path`, `test_uncompressed_path`, `test_species`, and @@ -242,7 +242,7 @@ with "(Recommended)" at the end of its label and place it first in the options l 2. Run the scaffold command: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh tool --config /tmp/scaffold-config.json --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh tool --config /tmp/scaffold-config.json --bactopia-path . --pretty ``` 3. The command creates all 16 files. Review the output to confirm which files were created. @@ -298,7 +298,7 @@ The templates produce correct scaffolds but many tools need customization: 5. **Run the linter** to catch structural issues before proceeding: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . ``` This runs `bactopia-lint` scoped to the new module, subworkflow, and workflow. Fix any FAILs before moving to Phase 5. Common issues: @@ -356,7 +356,7 @@ The templates produce correct scaffolds but many tools need customization: Test data paths are discovered dynamically from existing module tests using: ```bash -bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty +bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty ``` This scans `modules/*/tests/main.nf.test` for paths matching the input type and returns diff --git a/.claude/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh b/.agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh similarity index 100% rename from .claude/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh rename to .agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh diff --git a/.claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh b/.agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh similarity index 100% rename from .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh rename to .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh diff --git a/.claude/skills/add-module/SKILL.md b/.agents/skills/add-module/SKILL.md similarity index 96% rename from .claude/skills/add-module/SKILL.md rename to .agents/skills/add-module/SKILL.md index 12a387ffa..2810a961e 100644 --- a/.claude/skills/add-module/SKILL.md +++ b/.agents/skills/add-module/SKILL.md @@ -10,8 +10,8 @@ Scaffold a complete Bactopia module for a bioconda/conda-forge package, creating ## Prerequisites Before using this skill, read: -- `.claude/docs/standards/05-module-documentation.md` -- Module standards including module.config, schema.json, and test templates -- `.claude/docs/project/04-testing-framework.md` -- Testing framework details +- `.agents/docs/standards/05-module-documentation.md` -- Module standards including module.config, schema.json, and test templates +- `.agents/docs/project/04-testing-framework.md` -- Testing framework details ## Interactive Questioning @@ -41,7 +41,7 @@ Follow these phases in order. When unsure about ANYTHING, ask the user rather th 3. Run the lookup command: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty ``` 4. The output includes: @@ -101,7 +101,7 @@ with "(Recommended)" at the end of its label and place it first in the options l 3. **Run test-data discovery** based on the input type selected in Batch 1: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty ``` This returns species/accession combinations already used by similar modules, with pre-computed `test_data_path`, `test_uncompressed_path`, `test_species`, and @@ -207,7 +207,7 @@ with "(Recommended)" at the end of its label and place it first in the options l 2. Run the scaffold command: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh module --config /tmp/scaffold-config.json --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh module --config /tmp/scaffold-config.json --bactopia-path . --pretty ``` 3. The command creates 6 files: @@ -242,7 +242,7 @@ with "(Recommended)" at the end of its label and place it first in the options l 5. **Run the linter** to catch structural issues before proceeding: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . ``` This runs `bactopia-lint` scoped to the new module. Fix any FAILs before moving on. Common issues: @@ -283,7 +283,7 @@ with "(Recommended)" at the end of its label and place it first in the options l Test data paths are discovered dynamically from existing module tests using: ```bash -bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty +bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty ``` This scans `modules/*/tests/main.nf.test` for paths matching the input type and returns diff --git a/.claude/skills/add-subworkflow/SKILL.md b/.agents/skills/add-subworkflow/SKILL.md similarity index 96% rename from .claude/skills/add-subworkflow/SKILL.md rename to .agents/skills/add-subworkflow/SKILL.md index a392e3c9c..9b807cdea 100644 --- a/.claude/skills/add-subworkflow/SKILL.md +++ b/.agents/skills/add-subworkflow/SKILL.md @@ -10,7 +10,7 @@ Scaffold a Bactopia subworkflow that orchestrates one or more existing modules. ## Prerequisites - The module(s) this subworkflow will use must already exist under `modules/` -- Read `.claude/docs/standards/04-subworkflow-documentation.md` for documentation standards +- Read `.agents/docs/standards/04-subworkflow-documentation.md` for documentation standards ## Interactive Questioning @@ -54,12 +54,12 @@ at the end of its label and place it first in the options list. 2. **Run the lookup command** if package info is needed: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty ``` 3. **Determine the input type** from the primary module's inputs, then **run test-data discovery**: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty ``` This returns species/accession combinations already used by similar modules, with pre-computed `test_data_path`, `test_uncompressed_path`, `test_species`, and @@ -153,7 +153,7 @@ at the end of its label and place it first in the options list. 2. Run the scaffold command: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh subworkflow --config /tmp/scaffold-config.json --bactopia-path . --pretty + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh subworkflow --config /tmp/scaffold-config.json --bactopia-path . --pretty ``` 3. The command creates 5 files: @@ -187,7 +187,7 @@ at the end of its label and place it first in the options list. 4. **Run the linter** to catch structural issues before proceeding: ```bash - bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . + bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path . ``` This runs `bactopia-lint` scoped to the new subworkflow (and module if it exists). Fix any FAILs before moving on. Common issues: @@ -238,7 +238,7 @@ The scaffold generates one of three patterns based on the `aggregation.strategy` Test data paths are discovered dynamically from existing module tests using: ```bash -bash .claude/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty +bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty ``` This scans `modules/*/tests/main.nf.test` for paths matching the input type and returns diff --git a/.claude/skills/bump-versions/SKILL.md b/.agents/skills/bump-versions/SKILL.md similarity index 96% rename from .claude/skills/bump-versions/SKILL.md rename to .agents/skills/bump-versions/SKILL.md index 174af69f3..8b347da1e 100644 --- a/.claude/skills/bump-versions/SKILL.md +++ b/.agents/skills/bump-versions/SKILL.md @@ -27,7 +27,7 @@ Two classes of version-bearing files exist, and only one is this skill's concern 1. **Dry-run first.** Show the user exactly what will change before writing anything: ``` - python3 .claude/skills/bump-versions/scripts/bump_versions.py \ + python3 .agents/skills/bump-versions/scripts/bump_versions.py \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia --check ``` The script reads `versions.yml`, then reports each hand-maintained literal as @@ -39,7 +39,7 @@ Two classes of version-bearing files exist, and only one is this skill's concern 2. **Confirm, then apply.** Once the user is happy with the dry-run, drop `--check` to write the changes: ``` - python3 .claude/skills/bump-versions/scripts/bump_versions.py \ + python3 .agents/skills/bump-versions/scripts/bump_versions.py \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia ``` Only the version token inside each match is rewritten; runs are idempotent. @@ -52,7 +52,7 @@ Two classes of version-bearing files exist, and only one is this skill's concern 4. **Verify V001–V003.** Confirm the version gate is actually green: ``` - bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh \ + bash .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent ``` Read the `repo` component's results. A clean run lists **no** `V0xx` failures diff --git a/.claude/skills/bump-versions/evals/evals.json b/.agents/skills/bump-versions/evals/evals.json similarity index 100% rename from .claude/skills/bump-versions/evals/evals.json rename to .agents/skills/bump-versions/evals/evals.json diff --git a/.claude/skills/bump-versions/scripts/bump_versions.py b/.agents/skills/bump-versions/scripts/bump_versions.py similarity index 100% rename from .claude/skills/bump-versions/scripts/bump_versions.py rename to .agents/skills/bump-versions/scripts/bump_versions.py diff --git a/.claude/skills/merge-schemas/SKILL.md b/.agents/skills/merge-schemas/SKILL.md similarity index 98% rename from .claude/skills/merge-schemas/SKILL.md rename to .agents/skills/merge-schemas/SKILL.md index bd6714c78..3d728f493 100644 --- a/.claude/skills/merge-schemas/SKILL.md +++ b/.agents/skills/merge-schemas/SKILL.md @@ -35,7 +35,7 @@ Regenerate the `nextflow.config` and `nextflow_schema.json` files for one or mor 4. **Run `bactopia-merge-schemas` once per target** via the wrapper: ``` - bash .claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \ + bash .agents/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --wf \ --outdir \ diff --git a/.claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh b/.agents/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh similarity index 100% rename from .claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh rename to .agents/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh diff --git a/.claude/skills/project-status/SKILL.md b/.agents/skills/project-status/SKILL.md similarity index 98% rename from .claude/skills/project-status/SKILL.md rename to .agents/skills/project-status/SKILL.md index 8ad137850..97e28495b 100644 --- a/.claude/skills/project-status/SKILL.md +++ b/.agents/skills/project-status/SKILL.md @@ -11,7 +11,7 @@ Run the status script and interpret the output for the user. 1. Run `bactopia-status` via the wrapper script: ``` - bash .claude/skills/project-status/scripts/run-bactopia-status.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json + bash .agents/skills/project-status/scripts/run-bactopia-status.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json ``` 2. Parse the JSON output and present a clean, readable summary. Lead with: diff --git a/.claude/skills/project-status/scripts/run-bactopia-status.sh b/.agents/skills/project-status/scripts/run-bactopia-status.sh similarity index 100% rename from .claude/skills/project-status/scripts/run-bactopia-status.sh rename to .agents/skills/project-status/scripts/run-bactopia-status.sh diff --git a/.claude/skills/release-checklist/SKILL.md b/.agents/skills/release-checklist/SKILL.md similarity index 97% rename from .claude/skills/release-checklist/SKILL.md rename to .agents/skills/release-checklist/SKILL.md index a41fe1069..4f80b9e99 100644 --- a/.claude/skills/release-checklist/SKILL.md +++ b/.agents/skills/release-checklist/SKILL.md @@ -41,7 +41,7 @@ Present each result; never fix. Numbers below are the report's check IDs. Version-bearing file consistency is enforced by bactopia-lint's **repo rules**, not re-implemented in this skill. Run bactopia-lint once — the same run feeds checks 8 and 11 — and read the `repo`-tier results: ``` -bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path $BP --json --silent +bash .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path $BP --json --silent ``` Parse the `repo` component's `results[]` for rule IDs starting with `V`: @@ -54,7 +54,7 @@ Parse the `repo` component's `results[]` for rule IDs starting with `V`: The deterministic engine is run once and feeds checks 2, 12, 13: ``` -python3 .claude/skills/release-checklist/scripts/release_audit.py --bactopia-path $BP --json +python3 .agents/skills/release-checklist/scripts/release_audit.py --bactopia-path $BP --json ``` It returns `sibling_release_state` (check 12), `changelog` (check 13), `module_updates` (check 2), and `warnings[]` — surface any warnings. @@ -76,7 +76,7 @@ Report `log_timestamp`, `needs_update`, `needs_user_review`, and `up_to_date` fr For each of the 4 named workflows — `bactopia`, `teton`, `staphopia`, `cleanyerreads` (paths from `catalog.json.workflows[].path`) — regenerate into the scratch dir and diff against the committed copies: ``` -bash .claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \ +bash .agents/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \ --bactopia-path $BP --wf --outdir $AUDIT/ diff $AUDIT//nextflow.config diff $AUDIT//nextflow_schema.json @@ -87,7 +87,7 @@ The scratch dir is empty, so `--force` is not needed and nothing tracked is touc ### 4. Catalog & llms.txt freshness (read-only diff) ``` -bash .claude/skills/update-catalog/scripts/run-bactopia-catalog.sh \ +bash .agents/skills/update-catalog/scripts/run-bactopia-catalog.sh \ --bactopia-path $BP --output $AUDIT/catalog.json --pretty --llms-output $AUDIT/llms.txt diff $AUDIT/catalog.json $BP/catalog.json diff $AUDIT/llms.txt $BP/llms.txt @@ -103,10 +103,10 @@ In `$DOCS` (skip with a note if the repo is absent): - **(b) changelog mirror** — compare the top `## v` heading of `docs/changelog.md` to the main repo `CHANGELOG.md` top heading. A version mismatch is a WARN (mirror out of sync). - **(c) plugin pins** — V001 only scans the bactopia repo's `*.config` files, so the docs site is not covered by the linter. Grep it directly: `grep -rn 'nf-bactopia@' "$DOCS" --include='*.md' --include='*.mdx'` and flag any pin that lags `versions.yml: nf-bactopia` (currently `developers/nf-bactopia/index.mdx` pins `2.0.3`). WARN. -### 6. Docs sync (.claude/docs) +### 6. Docs sync (.agents/docs) ``` -bash .claude/skills/review-docs/scripts/run-bactopia-docs.sh --bactopia-path $BP --validate --json --silent +bash .agents/skills/review-docs/scripts/run-bactopia-docs.sh --bactopia-path $BP --validate --json --silent ``` Record `summary.fail`. Any FAIL ⇒ recommend `/review-docs`. @@ -114,7 +114,7 @@ Record `summary.fail`. Any FAIL ⇒ recommend `/review-docs`. ### 7. Citations integrity ``` -bash .claude/skills/review-citations/scripts/run-bactopia-citations.sh --bactopia-path $BP --validate --json --silent +bash .agents/skills/review-citations/scripts/run-bactopia-citations.sh --bactopia-path $BP --validate --json --silent ``` Record `summary.orphans_total` and `summary.missing_total`. Either > 0 ⇒ recommend `/review-citations`. (`expected_orphans` are informational, not failures.) @@ -139,7 +139,7 @@ Test runs live under `logs/run-tests//` (written by `/run-tests`); `b ``` LATEST_RUN=$(for d in $(ls -1dt "$BP"/logs/run-tests/[0-9]*/ 2>/dev/null); do [ -f "$d/summary.json" ] && basename "$d" && break; done) -bash .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path $BP --run "$LATEST_RUN" --silent +bash .agents/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path $BP --run "$LATEST_RUN" --silent ``` Also count how many `logs/run-tests/[0-9]*/` dirs are newer than `$LATEST_RUN` but lack a `summary.json` — those are incomplete/aborted runs worth flagging. @@ -209,7 +209,7 @@ The report is produced two ways from the same content: | 3 | Workflow configs & schemas | ... | ... | | 4 | Catalog & llms.txt freshness | ... | ... | | 5 | Docs-site (bactopia.io) state| ... | ... | -| 6 | Docs sync (.claude/docs) | ... | ... | +| 6 | Docs sync (.agents/docs) | ... | ... | | 7 | Citations | ... | ... | | 8 | GroovyDoc / lint | ... | ... | | 9 | Python lint (ruff) | ... | ... | diff --git a/.claude/skills/release-checklist/evals/evals.json b/.agents/skills/release-checklist/evals/evals.json similarity index 100% rename from .claude/skills/release-checklist/evals/evals.json rename to .agents/skills/release-checklist/evals/evals.json diff --git a/.claude/skills/release-checklist/scripts/release_audit.py b/.agents/skills/release-checklist/scripts/release_audit.py similarity index 100% rename from .claude/skills/release-checklist/scripts/release_audit.py rename to .agents/skills/release-checklist/scripts/release_audit.py diff --git a/.claude/skills/review-citations/SKILL.md b/.agents/skills/review-citations/SKILL.md similarity index 98% rename from .claude/skills/review-citations/SKILL.md rename to .agents/skills/review-citations/SKILL.md index a28a7cef1..5d53de1dd 100644 --- a/.claude/skills/review-citations/SKILL.md +++ b/.agents/skills/review-citations/SKILL.md @@ -22,7 +22,7 @@ Module and subworkflow `@citation` validation is handled by `bactopia-lint` rule 1. Run `bactopia-citations --validate` via the wrapper, asking for JSON so it's easy to parse: ``` - bash .claude/skills/review-citations/scripts/run-bactopia-citations.sh \ + bash .agents/skills/review-citations/scripts/run-bactopia-citations.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --validate --json --silent ``` @@ -166,4 +166,4 @@ Entries with this flag are intentionally unreferenced and surface in `expected_o ### When to redirect to other skills - Module or subworkflow `@citation` key typos → `/review-groovydoc` (rules M035, S019) -- Workflow GroovyDoc structure issues unrelated to citations → no skill yet; manual review against `.claude/docs/standards/06-workflow-documentation.md` +- Workflow GroovyDoc structure issues unrelated to citations → no skill yet; manual review against `.agents/docs/standards/06-workflow-documentation.md` diff --git a/.claude/skills/review-citations/scripts/run-bactopia-citations.sh b/.agents/skills/review-citations/scripts/run-bactopia-citations.sh similarity index 100% rename from .claude/skills/review-citations/scripts/run-bactopia-citations.sh rename to .agents/skills/review-citations/scripts/run-bactopia-citations.sh diff --git a/.claude/skills/review-docs/SKILL.md b/.agents/skills/review-docs/SKILL.md similarity index 95% rename from .claude/skills/review-docs/SKILL.md rename to .agents/skills/review-docs/SKILL.md index 263a6c512..24e0e6f8d 100644 --- a/.claude/skills/review-docs/SKILL.md +++ b/.agents/skills/review-docs/SKILL.md @@ -1,6 +1,6 @@ --- name: review-docs -description: Review staleness of reference docs under .claude/docs/ using bactopia-docs --validate. Detects deprecated patterns (residue from past migrations like flattenPaths, the 4-channel emission framing, meta:Map) and ground-truth violations (stale module/subworkflow/workflow counts, wrong Nextflow version, references to nonexistent bactopia-* commands or lint rule IDs, skill-inventory drift between 06-skills.md and .claude/skills/, broken markdown link targets). Use this skill whenever the user asks to review docs, check doc staleness, audit reference docs, find outdated documentation, verify doc claims, check if docs are current, or scan .claude/docs for drift after a migration. +description: Review staleness of reference docs under .agents/docs/ using bactopia-docs --validate. Detects deprecated patterns (residue from past migrations like flattenPaths, the 4-channel emission framing, meta:Map) and ground-truth violations (stale module/subworkflow/workflow counts, wrong Nextflow version, references to nonexistent bactopia-* commands or lint rule IDs, skill-inventory drift between 06-skills.md and .agents/skills/, broken markdown link targets). Use this skill whenever the user asks to review docs, check doc staleness, audit reference docs, find outdated documentation, verify doc claims, check if docs are current, or scan .agents/docs for drift after a migration. --- # Review Docs @@ -17,7 +17,7 @@ Two check families that don't fit the per-component lint rule model: - **D104** — Nextflow version (`nextflowVersion` in `nextflow.config`); informational mentions like `26.04+` or `until Nextflow X` are skipped. - **D105** — `` `bactopia-*` `` references inside backticks must resolve to a `[tool.poetry.scripts]` entry in `bactopia-py/pyproject.toml`. Bare prose mentions (`bactopia-tools`, `bactopia-py`) are ignored. - **D106** — `M0xx`/`S0xx`/`W0xx`/`MC0xx`/`JS0xx`/`FMT0xx` lint rule IDs must resolve to a `rid = "..."` assignment in `bactopia-py/bactopia/lint/rules/`. - - **D107** — skill inventory in [reference/06-skills.md](../../docs/reference/06-skills.md) must match `.claude/skills/*/SKILL.md`. Catches: skills on disk not listed in the table, rows referencing nonexistent skill directories, and purpose-cell drift from the SKILL.md `description:` first sentence. + - **D107** — skill inventory in [reference/06-skills.md](../../docs/reference/06-skills.md) must match `.agents/skills/*/SKILL.md`. Catches: skills on disk not listed in the table, rows referencing nonexistent skill directories, and purpose-cell drift from the SKILL.md `description:` first sentence. - **D108** — markdown link targets `[text](path)` must resolve to a real file. URLs and anchor-only links are skipped. Component-level checks live elsewhere: @@ -29,7 +29,7 @@ Component-level checks live elsewhere: 1. Run `bactopia-docs --validate` via the wrapper, asking for JSON so it's easy to parse: ``` - bash .claude/skills/review-docs/scripts/run-bactopia-docs.sh \ + bash .agents/skills/review-docs/scripts/run-bactopia-docs.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --validate --json --silent ``` @@ -41,7 +41,7 @@ Component-level checks live elsewhere: ```json { "bactopia_path": "/home/rpetit3/repos/bactopia/bactopia", - "docs_path": ".claude/docs", + "docs_path": ".agents/docs", "patterns_file": "data/docs-patterns.yml", "ground_truth": { "counts": {"modules": 97, "subworkflows": 88, "workflows": 70}, @@ -116,7 +116,7 @@ Component-level checks live elsewhere: Each pattern represents a migration that already landed; the doc is just out of sync. Three fix patterns: -- **Replace with current term**: most common case. `flattenPaths` → describe the current direct-emit pattern. `4-channel` → `2 channels (sample_outputs + run_outputs)`. `Tuple` → `Channel`. Read the surrounding paragraph before editing — sometimes the whole sentence needs rewriting, not just a token swap. Look at [reference/01-examples.md](.claude/docs/reference/01-examples.md) for the modern equivalents. +- **Replace with current term**: most common case. `flattenPaths` → describe the current direct-emit pattern. `4-channel` → `2 channels (sample_outputs + run_outputs)`. `Tuple` → `Channel`. Read the surrounding paragraph before editing — sometimes the whole sentence needs rewriting, not just a token swap. Look at [reference/01-examples.md](.agents/docs/reference/01-examples.md) for the modern equivalents. - **Delete entirely**: glossary entries for terms that no longer exist (e.g. the `flattenPaths` definition, the `Tuple` type entries) should be removed, not rephrased. Take the whole bullet/section. - **Mark as historical with inline ignore**: very rarely, a doc legitimately needs to mention a deprecated term — e.g. a "what changed in v4" note. Suppress the rule on that line with an HTML comment: @@ -160,7 +160,7 @@ Always confirm with the user before adding a pattern — false positives at the - **Suppression is a last resort.** `` is technical debt; prefer rewriting to remove the deprecated term entirely. The rare legitimate use is a deliberate historical reference (changelog, "what changed" notes). - **D105/D106 skip silently when bactopia-py isn't found.** If `ground_truth.bactopia_py_resolved` is `null`, those checks didn't run. Pass `--bactopia-py-path` explicitly if the sibling repo is in a non-default location. - The wrapper script auto-discovers `bactopia-docs` (checks PATH, then conda envs). No need to activate an env first. -- The CLI's `--bactopia-path` must point at the repo root so the validator can find `.claude/docs/`, `data/docs-patterns.yml`, `nextflow.config`, and the tier directories. +- The CLI's `--bactopia-path` must point at the repo root so the validator can find `.agents/docs/`, `data/docs-patterns.yml`, `nextflow.config`, and the tier directories. ## Quick reference @@ -189,7 +189,7 @@ patterns: ### CLI flags - `--bactopia-path PATH` — required, points at the bactopia repo root -- `--docs-path PATH` — relative to bactopia-path (default: `.claude/docs`) +- `--docs-path PATH` — relative to bactopia-path (default: `.agents/docs`) - `--patterns-file PATH` — relative to bactopia-path (default: `data/docs-patterns.yml`) - `--bactopia-py-path PATH` — override the sibling-repo discovery for D105/D106 - `--skip-path-check` — skip D108 (faster runs; useful when you know link health is fine) diff --git a/.claude/skills/review-docs/scripts/run-bactopia-docs.sh b/.agents/skills/review-docs/scripts/run-bactopia-docs.sh similarity index 100% rename from .claude/skills/review-docs/scripts/run-bactopia-docs.sh rename to .agents/skills/review-docs/scripts/run-bactopia-docs.sh diff --git a/.claude/skills/review-groovydoc/SKILL.md b/.agents/skills/review-groovydoc/SKILL.md similarity index 98% rename from .claude/skills/review-groovydoc/SKILL.md rename to .agents/skills/review-groovydoc/SKILL.md index 501103886..a552ecafe 100644 --- a/.claude/skills/review-groovydoc/SKILL.md +++ b/.agents/skills/review-groovydoc/SKILL.md @@ -11,7 +11,7 @@ Run bactopia-lint focused on GroovyDoc accuracy rules and present the results. 1. Run `bactopia-lint` via the wrapper script. By default, lint both modules and subworkflows: ``` - bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --quiet --json --silent + bash .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --quiet --json --silent ``` - For modules only: add `--no-subworkflows --no-workflows` - For subworkflows only: add `--no-modules --no-workflows` @@ -51,7 +51,7 @@ Run bactopia-lint focused on GroovyDoc accuracy rules and present the results. - S027: @output field descriptions must not exist for channel.empty() emits **Entry workflows (W-series):** - - No dedicated GroovyDoc-accuracy W-rules exist. Workflow GroovyDoc review is a manual pass — check the workflow main.nf against `.claude/docs/standards/06-workflow-documentation.md`, verify `@subworkflows` directory keys match actual `include { ... }` imports (e.g., `utils_bactopia-tools`, `bactopia_qc`), validate `@citation` keys against `data/citations.yml`, confirm `@input` names match declared `params { }`, and ensure each `@section` has ≥1 `@publish`. The one-off drift-check approach used on 2026-04-10 lived at `/tmp/workflow_drift_check.py` and reused `parse_groovydoc_full()` + `parse_includes()` from `bactopia-py/bactopia/nf.py`. + - No dedicated GroovyDoc-accuracy W-rules exist. Workflow GroovyDoc review is a manual pass — check the workflow main.nf against `.agents/docs/standards/06-workflow-documentation.md`, verify `@subworkflows` directory keys match actual `include { ... }` imports (e.g., `utils_bactopia-tools`, `bactopia_qc`), validate `@citation` keys against `data/citations.yml`, confirm `@input` names match declared `params { }`, and ensure each `@section` has ≥1 `@publish`. The one-off drift-check approach used on 2026-04-10 lived at `/tmp/workflow_drift_check.py` and reused `parse_groovydoc_full()` + `parse_includes()` from `bactopia-py/bactopia/nf.py`. 3. Present results as a clean summary: - **If all pass**: Report "All X modules/subworkflows have clean GroovyDoc" and stop diff --git a/.claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh b/.agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh similarity index 100% rename from .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh rename to .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh diff --git a/.claude/skills/review-tests/SKILL.md b/.agents/skills/review-tests/SKILL.md similarity index 99% rename from .claude/skills/review-tests/SKILL.md rename to .agents/skills/review-tests/SKILL.md index ec5b0ca5a..a76cc013e 100644 --- a/.claude/skills/review-tests/SKILL.md +++ b/.agents/skills/review-tests/SKILL.md @@ -17,7 +17,7 @@ profile against docker. 1. Run `bactopia-review-tests` via the wrapper script using the **default text output** (do NOT use `--json`): ``` - bash .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --silent + bash .agents/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --silent ``` If the user provided a timestamp argument (e.g., `/review-tests 20260324_081306`), add `--run 20260324_081306`. @@ -173,7 +173,7 @@ Baselines file: `conf/test-times.json`. Durations are **docker-based** (the CLI To update baselines after a clean all-pass run, add `--update-baselines`: ``` -bash .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --silent --update-baselines +bash .agents/skills/review-tests/scripts/run-bactopia-review-tests.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --silent --update-baselines ``` This writes actual runtimes from the current run into the baselines file and updates the `_meta.updated` timestamp. Only entries for tested components are updated; other tiers diff --git a/.claude/skills/review-tests/scripts/run-bactopia-review-tests.sh b/.agents/skills/review-tests/scripts/run-bactopia-review-tests.sh similarity index 100% rename from .claude/skills/review-tests/scripts/run-bactopia-review-tests.sh rename to .agents/skills/review-tests/scripts/run-bactopia-review-tests.sh diff --git a/.claude/skills/run-tests/SKILL.md b/.agents/skills/run-tests/SKILL.md similarity index 99% rename from .claude/skills/run-tests/SKILL.md rename to .agents/skills/run-tests/SKILL.md index f766c158c..bdfbb4848 100644 --- a/.claude/skills/run-tests/SKILL.md +++ b/.agents/skills/run-tests/SKILL.md @@ -22,7 +22,7 @@ responsibilities clearly separated -- do not try to do `/review-tests`' job here 2. **Invoke the wrapper script** with the resolved arguments: ``` - bash .claude/skills/run-tests/scripts/run-bactopia-test.sh \ + bash .agents/skills/run-tests/scripts/run-bactopia-test.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --test-data /home/rpetit3/repos/bactopia/bactopia-tests \ --outdir /home/rpetit3/repos/bactopia/bactopia \ @@ -243,7 +243,7 @@ Only the tiers that were tested have subdirectories in a given run. ### Wrapper script discovery order -The wrapper at `.claude/skills/run-tests/scripts/run-bactopia-test.sh` +The wrapper at `.agents/skills/run-tests/scripts/run-bactopia-test.sh` locates `bactopia-test` by checking, in order: 1. `bactopia-test` on `PATH` (respects an already-activated env) diff --git a/.claude/skills/run-tests/scripts/run-bactopia-test.sh b/.agents/skills/run-tests/scripts/run-bactopia-test.sh similarity index 100% rename from .claude/skills/run-tests/scripts/run-bactopia-test.sh rename to .agents/skills/run-tests/scripts/run-bactopia-test.sh diff --git a/.claude/skills/update-catalog/SKILL.md b/.agents/skills/update-catalog/SKILL.md similarity index 98% rename from .claude/skills/update-catalog/SKILL.md rename to .agents/skills/update-catalog/SKILL.md index 60c987364..35b66b1e8 100644 --- a/.claude/skills/update-catalog/SKILL.md +++ b/.agents/skills/update-catalog/SKILL.md @@ -17,7 +17,7 @@ Regenerate the machine-readable Bactopia component index (`catalog.json`) and th 2. **Run the wrapper** to regenerate both files in one invocation: ``` - bash .claude/skills/update-catalog/scripts/run-bactopia-catalog.sh \ + bash .agents/skills/update-catalog/scripts/run-bactopia-catalog.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --output /home/rpetit3/repos/bactopia/bactopia/catalog.json \ --pretty \ diff --git a/.claude/skills/update-catalog/scripts/run-bactopia-catalog.sh b/.agents/skills/update-catalog/scripts/run-bactopia-catalog.sh similarity index 76% rename from .claude/skills/update-catalog/scripts/run-bactopia-catalog.sh rename to .agents/skills/update-catalog/scripts/run-bactopia-catalog.sh index 7198d7cb0..28b0909ca 100755 --- a/.claude/skills/update-catalog/scripts/run-bactopia-catalog.sh +++ b/.agents/skills/update-catalog/scripts/run-bactopia-catalog.sh @@ -41,6 +41,19 @@ find_conda_env() { return 1 } +# Default --llms-output so llms.txt is always regenerated alongside catalog.json +# (bactopia-catalog only renders llms.txt when the flag is given). +if [[ " $* " != *" --llms-output "* ]]; then + llms_target="llms.txt" + prev="" + for arg in "$@"; do + case "$prev" in --bactopia-path) llms_target="$arg/llms.txt"; break ;; esac + case "$arg" in --bactopia-path=*) llms_target="${arg#*=}/llms.txt"; break ;; esac + prev="$arg" + done + set -- "$@" --llms-output "$llms_target" +fi + # 1. Check PATH if command -v bactopia-catalog &>/dev/null; then exec bactopia-catalog "$@" diff --git a/.claude/skills/update-datasets/SKILL.md b/.agents/skills/update-datasets/SKILL.md similarity index 97% rename from .claude/skills/update-datasets/SKILL.md rename to .agents/skills/update-datasets/SKILL.md index a3c7bce56..93a9e2dc7 100644 --- a/.claude/skills/update-datasets/SKILL.md +++ b/.agents/skills/update-datasets/SKILL.md @@ -27,7 +27,7 @@ carried it was removed. 1. **Currency gate (hard stop).** Confirm the module tool is the latest bioconda release before building: ``` - bash .claude/skills/update-module/scripts/run-bactopia-update.sh \ + bash .agents/skills/update-module/scripts/run-bactopia-update.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia --module amrfinderplus --json --silent ``` Parse the entry whose `tool == "ncbi-amrfinderplus"`. @@ -39,7 +39,7 @@ carried it was removed. 2. **Build.** Rebuild the database in the module's pinned container: ``` - bash .claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh \ + bash .agents/skills/update-datasets/scripts/build-amrfinderplus-db.sh \ --bactopia-path /home/rpetit3/repos/bactopia/bactopia ``` Add `--runtime singularity` if the user asks or docker is unavailable. This diff --git a/.claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh b/.agents/skills/update-datasets/scripts/build-amrfinderplus-db.sh similarity index 100% rename from .claude/skills/update-datasets/scripts/build-amrfinderplus-db.sh rename to .agents/skills/update-datasets/scripts/build-amrfinderplus-db.sh diff --git a/.claude/skills/update-module/SKILL.md b/.agents/skills/update-module/SKILL.md similarity index 98% rename from .claude/skills/update-module/SKILL.md rename to .agents/skills/update-module/SKILL.md index 19784450f..93ecca8c0 100644 --- a/.claude/skills/update-module/SKILL.md +++ b/.agents/skills/update-module/SKILL.md @@ -13,7 +13,7 @@ Check for newer versions of bioconda tools used in Bactopia modules and apply up ``` mkdir -p /home/rpetit3/repos/bactopia/bactopia/logs/module-updates TS=$(date +%Y%m%d_%H%M%S) - bash .claude/skills/update-module/scripts/run-bactopia-update.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent \ + bash .agents/skills/update-module/scripts/run-bactopia-update.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent \ | tee /home/rpetit3/repos/bactopia/bactopia/logs/module-updates/$TS.json ``` Parse the JSON from that file. If the user specified a module name, add `--module ` to the command **and do not write the record** (a filtered run is not a full-repo check — only an unfiltered scan is a valid `/release-checklist` freshness record). `logs/` is gitignored, so the record is scratch, not a tracked file. diff --git a/.claude/skills/update-module/scripts/run-bactopia-update.sh b/.agents/skills/update-module/scripts/run-bactopia-update.sh similarity index 100% rename from .claude/skills/update-module/scripts/run-bactopia-update.sh rename to .agents/skills/update-module/scripts/run-bactopia-update.sh diff --git a/.claude/settings.json b/.claude/settings.json deleted file mode 100644 index 6868c497d..000000000 --- a/.claude/settings.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "permissions": { - "allow": [ - "Bash(nf-test *)", - "WebFetch(domain:www.nf-test.com)", - "Bash(xargs ls:*)" - ], - "additionalDirectories": [ - "/home/rpetit3/.claude/projects/-home-rpetit3-repos-bactopia-bactopia", - "/home/rpetit3/repos/bactopia/bactopia-py", - "/home/rpetit3/repos/bactopia/nf-bactopia", - "/home/rpetit3/repos/bactopia/bactopia.github.io" - ] - } -} diff --git a/.claude/skills b/.claude/skills new file mode 120000 index 000000000..2b7a412b8 --- /dev/null +++ b/.claude/skills @@ -0,0 +1 @@ +../.agents/skills \ No newline at end of file diff --git a/.gitignore b/.gitignore index d32d876ab..0ab731365 100644 --- a/.gitignore +++ b/.gitignore @@ -26,10 +26,8 @@ data/conda/index.html data/conda/linux-64/ data/conda/noarch/ -# Claude -.claude/plans/ -.claude/handoffs/ -.claude/skills/*-workspace/ +# Agent skill workspaces +.agents/skills/*-workspace/ # temp v4 folders old-bactopia/ diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 000000000..de32a4ee8 --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,131 @@ +# Bactopia Pipeline Reference for AI Agents + +This document serves as the AI Context Master Map for the Bactopia pipeline, following the [agents.md](https://agents.md/) convention. It provides entry points to modular documentation for understanding the codebase structure, patterns, and conventions. + +## Project Overview + +Bactopia is a flexible pipeline for bacterial genome analysis. It follows a three-tier architecture: +- **Workflows** (Tier 1): User-facing entry points +- **Subworkflows** (Tier 2): Reusable orchestration components +- **Modules** (Tier 3): Individual tool implementations + +The pipeline uses standardized GroovyDoc documentation and static typing throughout all components. + +## Documentation Index + +### Standards and Conventions +- **[Style Guide & Templates](.agents/docs/standards/01-style-guide.md)** + - *Read this for*: GroovyDoc templates, header format, and tag ordering + - Visual formatting rules for all component types + +- **[Logic & Taxonomy](.agents/docs/standards/02-logic-rules.md)** + - *Read this for*: Determining complexity, input/output types + - Decision-making logic for component classification + +- **[Technical Specifications](.agents/docs/standards/03-technical-specs.md)** + - *Read this for*: Variable naming, type conventions, Path? optional inputs + - Implementation details and conventions + +- **[Subworkflow Documentation](.agents/docs/standards/04-subworkflow-documentation.md)** + - *Read this for*: Complete methodology for documenting subworkflows + - Step-by-step process with examples and best practices + +- **[Module Documentation](.agents/docs/standards/05-module-documentation.md)** + - *Read this for*: Complete methodology for documenting modules + - Detailed patterns and examples for individual tool implementations + +- **[Workflow Documentation](.agents/docs/standards/06-workflow-documentation.md)** + - *Read this for*: Complete methodology for documenting entry workflows + - User-facing documentation patterns with @publish and @section organization + +- **[Tier Architecture](.agents/docs/standards/07-tier-architecture.md)** + - *Read this for*: Formalized rules for workflows, subworkflows, and modules + - Tier responsibilities, allowed operations, plugin functions, ext system, catalog.json + +### Project Documentation +- **[Repository Structure](.agents/docs/project/01-repository-structure.md)** + - *Read this for*: Directory organization and three-tier architecture + - Physical layout of the codebase + +- **[Development Workflow](.agents/docs/project/02-development-workflow.md)** + - *Read this for*: Adding new tools and components + - Step-by-step development guide with checklist + +- **[Configuration System](.agents/docs/project/03-configuration-system.md)** + - *Read this for*: Understanding parameter hierarchy + - Configuration inheritance and profile management + +- **[Testing Framework](.agents/docs/project/04-testing-framework.md)** + - *Read this for*: Writing and running tests + - nf-test framework usage and patterns + +### Reference Materials +- **[Examples](.agents/docs/reference/01-examples.md)** + - *Read this for*: Concrete implementation examples + - Annotated examples of modules, subworkflows, and workflows + +- **[Troubleshooting](.agents/docs/reference/02-troubleshooting.md)** + - *Read this for*: Common error solutions + - Debugging tips and problem resolution + +- **[Glossary](.agents/docs/reference/03-glossary.md)** + - *Read this for*: Definitions of Bactopia-specific terms + - Quick reference for terminology and concepts + +- **[Plugin Functions](.agents/docs/reference/04-plugin-functions.md)** + - *Read this for*: Understanding `gather()` and `flattenPaths()` functions + - Channel manipulation utilities from nf-bactopia plugin + +- **[task.ext Properties](.agents/docs/reference/05-task-ext-properties.md)** + - *Read this for*: Configuring module behavior via task.ext + - Complete reference for all task.ext properties used in module.config files + +- **[Skills](.agents/docs/reference/06-skills.md)** + - *Read this for*: project-local skill inventory and when to invoke `skill-creator` + - Catalog of AI tooling built on top of `bactopia-*` CLIs + +## AI Agent Instructions + +When working with this codebase: + +1. **Read this Master Map first** to understand the structure +2. **Load only modules relevant to your current task** to maintain context efficiency +3. **For documenting modules**: Read [.agents/docs/standards/05-module-documentation.md](.agents/docs/standards/05-module-documentation.md) for complete methodology and examples +4. **For documenting subworkflows**: Read [.agents/docs/standards/04-subworkflow-documentation.md](.agents/docs/standards/04-subworkflow-documentation.md) for complete methodology and examples +5. **Always check** [.agents/docs/standards/03-technical-specs.md](.agents/docs/standards/03-technical-specs.md) for variable naming and technical conventions +6. **Always use the `bactopia-dev` conda env for all project tooling** — `ruff`, `bactopia-*` CLIs (`bactopia-lint`, `bactopia-test`, `bactopia-merge-schemas`, `bactopia-catalog`, `bactopia-citations`), and `nf-test`. Invoke via `conda run -n bactopia-dev ` (or activate the env first). Never report a check as SKIP because a tool is "not on PATH" without trying this env. + +## Quick Reference + +### Common Tasks + +**Adding a new tool**: +1. Read [Development Workflow](.agents/docs/project/02-development-workflow.md) +2. Follow the step-by-step guide +3. Use templates from [Module Documentation](.agents/docs/standards/05-module-documentation.md) + +**Debugging type errors**: +1. Check [Technical Specifications](.agents/docs/standards/03-technical-specs.md) +2. Review [Troubleshooting](.agents/docs/reference/02-troubleshooting.md) +3. Look for Path? optional input patterns + +**Understanding architecture**: +1. Start with [Repository Structure](.agents/docs/project/01-repository-structure.md) +2. Review three-tier architecture +3. Study [Examples](.agents/docs/reference/01-examples.md) + +**Creating or editing a skill**: +1. Use the `skill-creator` skill — do not hand-scaffold `SKILL.md` files +2. See [Skills](.agents/docs/reference/06-skills.md) for the project's skill conventions and inventory + +### Key Patterns + +**Module inputs**: Record-typed with named parameters (e.g., `record(meta: Record, fna: Path)`) +**Module outputs**: Single `record()` with named fields (downstream) + generic fields (publishing) +**Subworkflow outputs**: Emit `sample_outputs` (module record passthrough) and `run_outputs` (aggregated) +**Optional parameters**: Use `Path?` types with `?` suffix in GroovyDoc + +### Important Reminders +- **Use `file()` for single files, `files()` for multiple** +- **Follow existing patterns** - Don't reinvent unless necessary +- **Always use 4 spaces for indentation** in all code blocks and lists, with the exception of YAML files which use 2 spaces diff --git a/CHANGELOG.md b/CHANGELOG.md index b8f11da58..f94f48a3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,9 @@ sidebar_position: 5000 - cleanyerreads workflow supports `--use_deacon` flag for host read removal - Added `params.bactopia_dir` which anchors to the Bactopia repo root so `data/` can be reference by all workflows - Centralized the pipeline version and `nf-bactopia@` plugin pin for module/subworkflow tests into `conf/test_base.config`; each `tests/nextflow.config` now `includeConfig`s it instead of repeating the values, so a version bump touches one file +- Migrated AI agent context to the community-standard layout: `CLAUDE.md` is now `AGENTS.md` (agents.md convention, read natively by omp/pi, Kimi Code, Codex, Cursor, and others), and `.claude/docs` + `.claude/skills` moved to `.agents/docs` + `.agents/skills` + - Claude Code compatibility is preserved via a one-line `CLAUDE.md` shim (`@AGENTS.md`) and a `.claude/skills` symlink + - `llms.txt` template updated: module layout corrected (`module.config`/`schema.json`, not `meta.yml`) and the full `.agents/docs/` index is now listed ### `Fixed` diff --git a/CLAUDE.md b/CLAUDE.md index 4ec3faf89..43c994c2d 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -1,131 +1 @@ -# Bactopia Pipeline Reference for Claude - -This document serves as the AI Context Master Map for the Bactopia pipeline. It provides entry points to modular documentation for understanding the codebase structure, patterns, and conventions. - -## Project Overview - -Bactopia is a flexible pipeline for bacterial genome analysis. It follows a three-tier architecture: -- **Workflows** (Tier 1): User-facing entry points -- **Subworkflows** (Tier 2): Reusable orchestration components -- **Modules** (Tier 3): Individual tool implementations - -The pipeline uses standardized GroovyDoc documentation and static typing throughout all components. - -## Documentation Index - -### Standards and Conventions -- **[Style Guide & Templates](.claude/docs/standards/01-style-guide.md)** - - *Read this for*: GroovyDoc templates, header format, and tag ordering - - Visual formatting rules for all component types - -- **[Logic & Taxonomy](.claude/docs/standards/02-logic-rules.md)** - - *Read this for*: Determining complexity, input/output types - - Decision-making logic for component classification - -- **[Technical Specifications](.claude/docs/standards/03-technical-specs.md)** - - *Read this for*: Variable naming, type conventions, Path? optional inputs - - Implementation details and conventions - -- **[Subworkflow Documentation](.claude/docs/standards/04-subworkflow-documentation.md)** - - *Read this for*: Complete methodology for documenting subworkflows - - Step-by-step process with examples and best practices - -- **[Module Documentation](.claude/docs/standards/05-module-documentation.md)** - - *Read this for*: Complete methodology for documenting modules - - Detailed patterns and examples for individual tool implementations - -- **[Workflow Documentation](.claude/docs/standards/06-workflow-documentation.md)** - - *Read this for*: Complete methodology for documenting entry workflows - - User-facing documentation patterns with @publish and @section organization - -- **[Tier Architecture](.claude/docs/standards/07-tier-architecture.md)** - - *Read this for*: Formalized rules for workflows, subworkflows, and modules - - Tier responsibilities, allowed operations, plugin functions, ext system, catalog.json - -### Project Documentation -- **[Repository Structure](.claude/docs/project/01-repository-structure.md)** - - *Read this for*: Directory organization and three-tier architecture - - Physical layout of the codebase - -- **[Development Workflow](.claude/docs/project/02-development-workflow.md)** - - *Read this for*: Adding new tools and components - - Step-by-step development guide with checklist - -- **[Configuration System](.claude/docs/project/03-configuration-system.md)** - - *Read this for*: Understanding parameter hierarchy - - Configuration inheritance and profile management - -- **[Testing Framework](.claude/docs/project/04-testing-framework.md)** - - *Read this for*: Writing and running tests - - nf-test framework usage and patterns - -### Reference Materials -- **[Examples](.claude/docs/reference/01-examples.md)** - - *Read this for*: Concrete implementation examples - - Annotated examples of modules, subworkflows, and workflows - -- **[Troubleshooting](.claude/docs/reference/02-troubleshooting.md)** - - *Read this for*: Common error solutions - - Debugging tips and problem resolution - -- **[Glossary](.claude/docs/reference/03-glossary.md)** - - *Read this for*: Definitions of Bactopia-specific terms - - Quick reference for terminology and concepts - -- **[Plugin Functions](.claude/docs/reference/04-plugin-functions.md)** - - *Read this for*: Understanding `gather()` and `flattenPaths()` functions - - Channel manipulation utilities from nf-bactopia plugin - -- **[task.ext Properties](.claude/docs/reference/05-task-ext-properties.md)** - - *Read this for*: Configuring module behavior via task.ext - - Complete reference for all task.ext properties used in module.config files - -- **[Skills](.claude/docs/reference/06-skills.md)** - - *Read this for*: project-local skill inventory and when to invoke `skill-creator` - - Catalog of AI tooling built on top of `bactopia-*` CLIs - -## AI Agent Instructions - -When working with this codebase: - -1. **Read this Master Map first** to understand the structure -2. **Load only modules relevant to your current task** to maintain context efficiency -3. **For documenting modules**: Read [.claude/docs/standards/05-module-documentation.md](.claude/docs/standards/05-module-documentation.md) for complete methodology and examples -4. **For documenting subworkflows**: Read [.claude/docs/standards/04-subworkflow-documentation.md](.claude/docs/standards/04-subworkflow-documentation.md) for complete methodology and examples -5. **Always check** [.claude/docs/standards/03-technical-specs.md](.claude/docs/standards/03-technical-specs.md) for variable naming and technical conventions -6. **Always use the `bactopia-dev` conda env for all project tooling** — `ruff`, `bactopia-*` CLIs (`bactopia-lint`, `bactopia-test`, `bactopia-merge-schemas`, `bactopia-catalog`, `bactopia-citations`), and `nf-test`. Invoke via `conda run -n bactopia-dev ` (or activate the env first). Never report a check as SKIP because a tool is "not on PATH" without trying this env. - -## Quick Reference - -### Common Tasks - -**Adding a new tool**: -1. Read [Development Workflow](.claude/docs/project/02-development-workflow.md) -2. Follow the step-by-step guide -3. Use templates from [Module Documentation](.claude/docs/standards/05-module-documentation.md) - -**Debugging type errors**: -1. Check [Technical Specifications](.claude/docs/standards/03-technical-specs.md) -2. Review [Troubleshooting](.claude/docs/reference/02-troubleshooting.md) -3. Look for Path? optional input patterns - -**Understanding architecture**: -1. Start with [Repository Structure](.claude/docs/project/01-repository-structure.md) -2. Review three-tier architecture -3. Study [Examples](.claude/docs/reference/01-examples.md) - -**Creating or editing a skill**: -1. Use the `skill-creator` skill — do not hand-scaffold `SKILL.md` files -2. See [Skills](.claude/docs/reference/06-skills.md) for the project's skill conventions and inventory - -### Key Patterns - -**Module inputs**: Record-typed with named parameters (e.g., `record(meta: Record, fna: Path)`) -**Module outputs**: Single `record()` with named fields (downstream) + generic fields (publishing) -**Subworkflow outputs**: Emit `sample_outputs` (module record passthrough) and `run_outputs` (aggregated) -**Optional parameters**: Use `Path?` types with `?` suffix in GroovyDoc - -### Important Reminders -- **Use `file()` for single files, `files()` for multiple** -- **Follow existing patterns** - Don't reinvent unless necessary -- **Always use 4 spaces for indentation** in all code blocks and lists, with the exception of YAML files which use 2 spaces +@AGENTS.md diff --git a/data/docs-patterns.yml b/data/docs-patterns.yml index 988c554bc..22e943a9c 100644 --- a/data/docs-patterns.yml +++ b/data/docs-patterns.yml @@ -2,7 +2,7 @@ # # Each entry flags a phrase that is no longer current — usually residue # from a past migration. Validator (`bactopia.lint.docs.validate_docs`) -# greps every line of every doc under `.claude/docs/` against these +# greps every line of every doc under `.agents/docs/` against these # patterns; matches surface as D0xx FAILs. # # Schema (per entry): diff --git a/llms.txt b/llms.txt index 31d478f32..2ea43d2eb 100644 --- a/llms.txt +++ b/llms.txt @@ -36,7 +36,8 @@ All components use standardized GroovyDoc documentation and static typing. 104 tool-specific modules live under `modules/`. Each module directory contains: - `main.nf`: Process definition with GroovyDoc header -- `meta.yml`: Tool metadata, inputs, outputs, and parameter descriptions +- `module.config`: Default parameters and `task.ext` configuration +- `schema.json`: JSON Schema for the module's parameters - `tests/`: nf-test test cases Key module categories: @@ -53,17 +54,24 @@ Key module categories: ## AI Agent Documentation -- [CLAUDE.md](CLAUDE.md): Master map for AI agents — architecture, conventions, and documentation index -- [.claude/docs/standards/01-style-guide.md](.claude/docs/standards/01-style-guide.md): GroovyDoc templates and formatting rules -- [.claude/docs/standards/02-logic-rules.md](.claude/docs/standards/02-logic-rules.md): Component classification logic -- [.claude/docs/standards/03-technical-specs.md](.claude/docs/standards/03-technical-specs.md): Variable naming, types, Path? optional inputs -- [.claude/docs/standards/04-subworkflow-documentation.md](.claude/docs/standards/04-subworkflow-documentation.md): Subworkflow documentation methodology -- [.claude/docs/standards/05-module-documentation.md](.claude/docs/standards/05-module-documentation.md): Module documentation methodology -- [.claude/docs/standards/07-tier-architecture.md](.claude/docs/standards/07-tier-architecture.md): Tier architecture rules, plugin functions, ext system, catalog.json -- [.claude/docs/project/01-repository-structure.md](.claude/docs/project/01-repository-structure.md): Full directory layout -- [.claude/docs/project/02-development-workflow.md](.claude/docs/project/02-development-workflow.md): Step-by-step guide for adding new tools -- [.claude/docs/reference/01-examples.md](.claude/docs/reference/01-examples.md): Annotated implementation examples -- [.claude/docs/reference/06-skills.md](.claude/docs/reference/06-skills.md): Project skill inventory and when to invoke skill-creator +- [AGENTS.md](AGENTS.md): Master map for AI agents — architecture, conventions, and documentation index +- [.agents/docs/standards/01-style-guide.md](.agents/docs/standards/01-style-guide.md): GroovyDoc templates and formatting rules +- [.agents/docs/standards/02-logic-rules.md](.agents/docs/standards/02-logic-rules.md): Component classification logic +- [.agents/docs/standards/03-technical-specs.md](.agents/docs/standards/03-technical-specs.md): Variable naming, types, Path? optional inputs +- [.agents/docs/standards/04-subworkflow-documentation.md](.agents/docs/standards/04-subworkflow-documentation.md): Subworkflow documentation methodology +- [.agents/docs/standards/05-module-documentation.md](.agents/docs/standards/05-module-documentation.md): Module documentation methodology +- [.agents/docs/standards/06-workflow-documentation.md](.agents/docs/standards/06-workflow-documentation.md): Workflow documentation methodology +- [.agents/docs/standards/07-tier-architecture.md](.agents/docs/standards/07-tier-architecture.md): Tier architecture rules, plugin functions, ext system, catalog.json +- [.agents/docs/project/01-repository-structure.md](.agents/docs/project/01-repository-structure.md): Full directory layout +- [.agents/docs/project/02-development-workflow.md](.agents/docs/project/02-development-workflow.md): Step-by-step guide for adding new tools +- [.agents/docs/project/03-configuration-system.md](.agents/docs/project/03-configuration-system.md): Parameter hierarchy and profile management +- [.agents/docs/project/04-testing-framework.md](.agents/docs/project/04-testing-framework.md): nf-test framework usage and patterns +- [.agents/docs/reference/01-examples.md](.agents/docs/reference/01-examples.md): Annotated implementation examples +- [.agents/docs/reference/02-troubleshooting.md](.agents/docs/reference/02-troubleshooting.md): Common error solutions +- [.agents/docs/reference/03-glossary.md](.agents/docs/reference/03-glossary.md): Bactopia-specific terminology +- [.agents/docs/reference/04-plugin-functions.md](.agents/docs/reference/04-plugin-functions.md): nf-bactopia channel utilities +- [.agents/docs/reference/05-task-ext-properties.md](.agents/docs/reference/05-task-ext-properties.md): task.ext reference for module.config files +- [.agents/docs/reference/06-skills.md](.agents/docs/reference/06-skills.md): Project skill inventory (.agents/skills/) and when to invoke skill-creator ## Key Patterns for Agents From 82a086dc1a5bec28a6795a2af7c215174c3e7f9f Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 15:50:21 -0600 Subject: [PATCH 35/43] more context updates --- .agents/docs/standards/03-technical-specs.md | 60 ++++++++++++++++++++ .agents/skills/add-bactopia-tool/SKILL.md | 11 ++-- 2 files changed, 66 insertions(+), 5 deletions(-) diff --git a/.agents/docs/standards/03-technical-specs.md b/.agents/docs/standards/03-technical-specs.md index 8e3c2124f..59afa263e 100644 --- a/.agents/docs/standards/03-technical-specs.md +++ b/.agents/docs/standards/03-technical-specs.md @@ -505,6 +505,66 @@ GATHER is the only module that appends a `*???-` suffix — it runs before | `prokka`, `agrvate`, `bakta/run` | `staging/fna/*` | Single assembly staging | | `defensefinder/run` | `staging/faa/*` | Protein FASTA staging | +## Input Decompression Pattern + +Many tools do not accept gzip-compressed input (or cannot follow symlinks). Since assemblies +and other inputs may arrive either compressed (`.gz`) or plain, modules that need a real file +on disk use a standard decompress-or-copy guard. This is the convention used across ~34 modules +(e.g., `agrvate`, `ectyper`, `mobsuite/recon`, `checkm2/predict`, `clonalframeml`). + +In the Groovy script block, before the shell heredoc: + +```groovy +def is_compressed = fna.getName().endsWith(".gz") ? true : false +def fna_name = fna.getName().replace(".gz", "") +``` + +In the shell block: + +```bash +if [ "${is_compressed}" == "true" ]; then + gzip -c -d ${fna} > ${fna_name} +fi +``` + +Then pass `${fna_name}` to the tool. Some tools also cannot follow symlinks, so the `else` +branch copies the real file (`cp -L ${fna} ${fna_name}`); include it only when the tool needs +a bare-named file at the task root in the uncompressed case too (e.g., `agrvate`). + +### `getName()` vs `fileName.name` + +`Path.getName()` (== the `.name` property) returns the path **relative to the task directory**, +not necessarily the bare filename. For a normally-staged (flat) input the two are identical: + +```groovy +flat.getName() // a.fna.gz +flat.fileName.name // a.fna.gz (same) +``` + +But for an input placed in a subdirectory via `stageAs 'staging/fna/*'`, `getName()` keeps the +subdir prefix while `fileName.name` strips it: + +```groovy +sub.getName() // staging/fna/b.fna.gz +sub.fileName.name // b.fna.gz +``` + +(Verified empirically; see the Nextflow [Path docs](https://docs.seqera.io/nextflow/reference/stdlib-types/path) — "Use `fileName.name` for task paths to get only the file name.") + +**Prefer `getName()`** — it is the established default and works for the common flat-input case: +- Suffix checks (`.endsWith(".gz")`, `is_tarball` detection) are unaffected by a subdir prefix, so `getName()` is always fine there. +- When a module decompresses/reads the staged file **in place** (no `cp`), the subdir-relative + path from `getName()` is exactly what the shell needs (e.g., `prokka` — the `${fna_name}` + it builds must resolve to the staged `staging/fna/...` file). + +**Use `fileName.name` only** when the module copies/decompresses to a **fresh bare-named local +file** the tool then reads (explicit `if/else` with `cp -L`), where a `staging/fna/` prefix +would corrupt the output name (e.g., `agrvate`, `gamma`). The rule of thumb: match the shell +strategy — `fileName.name` for copy-to-local, `getName()` for read-in-place. + +Do NOT use ad-hoc alternatives like `fna.getName()[0..-4]` or inline `gunzip -c` behind a +`[[ ... == *.gz ]]` shell test — keep the guard uniform. + ## Database Handling Patterns Many modules accept external databases. The codebase supports two formats: diff --git a/.agents/skills/add-bactopia-tool/SKILL.md b/.agents/skills/add-bactopia-tool/SKILL.md index a9dd6380b..e8bddc255 100644 --- a/.agents/skills/add-bactopia-tool/SKILL.md +++ b/.agents/skills/add-bactopia-tool/SKILL.md @@ -276,15 +276,16 @@ The templates produce correct scaffolds but many tools need customization: ```bash if [ "${is_compressed}" == "true" ]; then gzip -c -d ${fna} > ${fna_name} - else - cp -L ${fna} ${fna_name} fi ``` Then use `${fna_name}` as the input filename for the tool command. This pattern is - used consistently across modules (e.g., staphopiasccmec, traitar). Do NOT use - alternative approaches like `fna.getName()[0..-4]` or inline `gunzip -c` with - `if [[ ... == *.gz ]]` shell tests. + used consistently across modules (e.g., staphopiasccmec, traitar). Prefer `fna.getName()`; + it returns the task-relative staged path, which is what read-in-place tools need. Use + `fna.fileName.name` only when you copy/decompress to a fresh bare-named local file (explicit + `if/else` with `cp -L`) and this module `stageAs`'s the input into a subdir, where a + `staging/fna/` prefix would corrupt the output name (e.g., `agrvate`, `gamma`). Do NOT use + alternatives like `fna.getName()[0..-4]` or inline `gunzip -c` with `if [[ ... == *.gz ]]`. 2. **Module `module.config`** -- review the `ext.args` construction: - Verify boolean/string/integer flag handling is correct for each parameter From 2d6b839b6e13abf1134ec05fa2d44dd74ff937f0 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 19:34:51 -0600 Subject: [PATCH 36/43] update run-tests skill for latest changes --- .agents/skills/run-tests/SKILL.md | 143 ++++++++++++++++++++---------- 1 file changed, 96 insertions(+), 47 deletions(-) diff --git a/.agents/skills/run-tests/SKILL.md b/.agents/skills/run-tests/SKILL.md index bdfbb4848..840bfa036 100644 --- a/.agents/skills/run-tests/SKILL.md +++ b/.agents/skills/run-tests/SKILL.md @@ -12,6 +12,14 @@ timestamped `logs/run-tests/{timestamp}/` directory; `/review-tests` then **inte that directory (grouping failures, reading stdout files, etc.). Keep the two responsibilities clearly separated -- do not try to do `/review-tests`' job here. +**Every run is a 4-profile matrix.** `bactopia-test` no longer takes a +`--profile` flag. For each selected component it tests `docker`, `conda`, +`singularity_galaxy`, and `singularity_pull`: docker validates (or generates) +the snapshot and the other three validate against it, surfacing runtime drift +without rewriting tests. Conda envs and Singularity images are **pre-built +serially** (from `--cachedir`) before the parallel test phase, so even a +single-component run pays that build/setup cost up front. + ## Steps 1. **Resolve `--tier` and `--include` from what the user said.** Use the @@ -26,8 +34,7 @@ responsibilities clearly separated -- do not try to do `/review-tests`' job here --bactopia-path /home/rpetit3/repos/bactopia/bactopia \ --test-data /home/rpetit3/repos/bactopia/bactopia-tests \ --outdir /home/rpetit3/repos/bactopia/bactopia \ - --profile docker \ - --keep \ + --cachedir /data/cache \ [--tier TIER] \ --include COMPONENT ``` @@ -38,9 +45,10 @@ responsibilities clearly separated -- do not try to do `/review-tests`' job here whose name contains `snippy`. 3. **Present the CLI's live output directly.** `bactopia-test` produces a Rich - table with per-component status, durations, and a final summary. Relay it - without reformatting. Do not parse JSON, do not re-tabulate, do not read the - stdout files the CLI writes. + table with per-component, per-profile status (docker / conda / + singularity_galaxy / singularity_pull), durations, and a final summary. + Relay it without reformatting. Do not parse JSON, do not re-tabulate, do not + read the stdout files the CLI writes. 4. **After the run finishes**, extract the run timestamp and hand off to `/review-tests`. See the "After the run" section. @@ -76,39 +84,40 @@ These flags are always added without asking the user: | ----------------- | -------------------------------------------- | ----------------------------------------------------------------------------- | | `--bactopia-path` | `/home/rpetit3/repos/bactopia/bactopia` | Canonical repo location on this machine. | | `--test-data` | `/home/rpetit3/repos/bactopia/bactopia-tests`| Canonical test-data location; sets `BACTOPIA_TESTS`. | -| `--profile` | `docker` | Default execution profile. Docker is the baseline for reproducible tests. | -| `--keep` | *(always)* | Preserves `.nf-test/` dirs and logs on pass; `/review-tests` needs them. | +| `--cachedir` | `/data/cache` | Holds pre-built `conda/` and `singularity/` env caches on this host (the CLI default `~/.bactopia` is empty here). | | `--outdir` | `/home/rpetit3/repos/bactopia/bactopia` | So `logs/run-tests/{timestamp}/` lands at the repo root, where `/review-tests` reads. | ## When to ask the user first (never auto-fill) | Flag | Policy | | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `--condadir` | Only add if the user explicitly asked for `--profile conda`. **Ask the user** for the cache path before running; do not guess. | -| `--singularity_cache`| Only add if the user explicitly asked for `--profile singularity`. **Ask the user** for the cache path before running; do not guess. | -| `--generate` | **Never** add unless the user's request contains one of: `--generate`, "generate mode", "regenerate snapshots", or "update snapshots". Destructively deletes snapshots. | -| `--jobs N` | Pass through if the user specified a number (e.g. "with 32 jobs"); otherwise omit and let the CLI default (`max(1, nproc // 4)`) apply. | +| `--generate` | **Never** add unless the user's request contains one of: `--generate`, "generate mode", "regenerate snapshots", or "update snapshots". It **overwrites the committed docker `.snap`** for the tested components. | +| `--force-rebuild` | Only add if the user explicitly asks to rebuild environments (or a `build_failed` was diagnosed). Forces a rebuild of existing Conda envs and Singularity images -- slow. | +| `--jobs N` | Pass through if the user specified a number (e.g. "with 16 jobs"); otherwise omit and let the CLI default (`32`) apply. This is components-in-parallel; the 4 profiles within a component run sequentially. | ## Important Reminders These are the non-negotiable rules. Violating any of them can burn hours of time or delete work the user cares about. -- **CRITICAL: never run with no component filter.** The CLI defaults to - `--tier all` with no `--include`, which runs the entire test suite across - 96 modules + 87 subworkflows + 69 workflows. That is expensive and is not - what this skill is for. If the user asks to "run tests" without naming a - component, **stop and ask** which module / subworkflow / workflow they want. +- **CRITICAL: never run with no component filter.** With no `--include`, the CLI + tests every component (250+ across modules, subworkflows, and workflows) and + each one runs the full 4-profile matrix -- plus a serial env pre-build phase. + That is very expensive and is not what this skill is for. If the user asks to + "run tests" without naming a component, **stop and ask** which module / + subworkflow / workflow they want. - **NEVER pass `--generate`** unless the user explicitly asked for it with the literal flag name or the phrases "generate mode", "regenerate - snapshots", or "update snapshots". `--generate` deletes existing snapshot - files and re-runs each test twice. The deletion is not recoverable from - within the skill. + snapshots", or "update snapshots". `--generate` forces regeneration of the + docker snapshot, **overwriting the committed `.snap`** for the tested + components. (Without it, a missing snapshot is still generated automatically; + an existing one is validated, not touched.) -- **ALWAYS pass `--keep`.** On pass, the CLI cleans up `.nf-test/` work - directories by default; `--keep` preserves them. `/review-tests` may need - to read into them to diagnose undeclared outputs or assertion mismatches. +- **ALWAYS pass `--cachedir /data/cache`.** The pre-built `conda/` and + `singularity/` env caches live there on this host. The CLI default + (`~/.bactopia`) is empty, so omitting it forces every environment to rebuild + from scratch -- hours of wasted work. - **ALWAYS pass `--outdir /home/rpetit3/repos/bactopia/bactopia`** so that `logs/run-tests/{timestamp}/` is written at the bactopia repo root. `/review-tests` @@ -122,26 +131,53 @@ time or delete work the user cares about. not needed here. - **Do NOT pass `--fail-fast`** unless the user explicitly asks. The default - "run everything, report all failures at the end" behavior is what - `/review-tests` expects to consume. + "run every component, report all failures at the end" behavior is what + `/review-tests` expects to consume. (`--fail-fast` stops on the first + component with any failing profile.) - **Do NOT interpret failures in detail here.** Do not read - `.stdout.txt`, `.stderr.txt`, `.outputs.txt`, or `nextflow.log` files. Do + `stdout.txt`, `stderr.txt`, `outputs.txt`, or `nextflow.log` files. Do not group failures by type. Do not recommend fixes. That is deliberately reserved for `/review-tests` so the two skills stay loosely coupled and each has a single clear job. -- **Profile switching requires extra info.** If the user asks for - `--profile singularity` or `--profile conda`, switch profiles **and** ask - them for the corresponding `--singularity_cache` or `--condadir` path - before invoking the wrapper. Do not guess. +- **There is no `--profile` flag anymore.** Every run tests all four profiles. + If the user wants to re-check a single drifting/timed-out profile cell (e.g. + "re-run stecfinder's conda test"), you still run the whole component -- the + matrix always covers that profile -- and point them at that profile's row in + the output. + +- **A `timeout` can be an intermittent *hang*, not a too-small budget -- do not + assume raising `-tm` will let it finish.** Per-component timeout = + `min(expected_seconds * -tm, --timeout)`. A cell that hangs never completes: + the task is killed by SIGTERM at the cap, so a bigger budget only makes it + hang longer. Confirmed example: `stecfinder`'s conda profile has repeatedly + wedged on its third case -- the task runs the full ~184s (`46.1 * 4`) and is + killed (**exit 143**, `succeededCount=0; abortedCount=1`, no `Task completed`, + 0-byte outputs), yet the whole component passes in ~24s (docker ~24s) when the + hang doesn't recur. This is a **known intermittent hang to keep an eye on**, + not slowness and not a baseline problem. + When a cell reports `timeout`, inspect the work tree to classify it, then act: + - **Hang** (`{profile}/.nf-test/.../work/**/.exitcode` = `143`, empty/0-byte + outputs, no `Task completed` in `meta/nextflow.log`): the tool/task never + returned control to nextflow/nf-test. **Do NOT** raise `-tm` or + `--update-baselines` -- neither addresses a hang. In a real pipeline run + Nextflow's own task retries absorb an intermittent hang like this, so no + code change is required unless it becomes persistent. If it does recur + often, escalate to a **cross-environment deep dive** (compare the docker + vs conda vs singularity envs -- program versions, dependency pins) to find + what differs on the wedging profile. + - **Genuine slow-but-completes** (task reaches `COMPLETED` just past the + budget): re-run with a raised `-tm`; if it then passes, the budget was the + issue. Only this case warrants a baseline/multiplier adjustment. ## After the run When `bactopia-test` finishes, do these four things -- nothing more: -1. **Report overall pass/fail counts** from the CLI's final summary table - (it prints a row-count breakdown by status). +1. **Report the status breakdown** from the CLI's final summary table. It is a + per-profile matrix (docker / conda / singularity_galaxy / singularity_pull); + report the counts as shown. 2. **Extract the run timestamp.** The CLI prints the path to the logs directory, which ends in a `YYYYMMDD_HHMMSS` directory (e.g. @@ -200,13 +236,15 @@ Defaults in parentheses. - `--exclude` — comma-separated component names (default: none) **Execution** -- `--profile` — `docker` / `singularity` / `conda` (default: `docker`) -- `--condadir` — conda cache dir (default: `${BACTOPIA_CACHEDIR}/conda`) -- `--singularity_cache` — singularity cache dir (default: `${BACTOPIA_CACHEDIR}/singularity`) -- `--generate` — delete snapshots and run twice (default: off) -- `--jobs` — parallel workers (default: `max(1, nproc // 4)`) -- `--fail-fast` — stop on first failure (default: off) -- `--timeout` — per-test timeout in **minutes**, 0 to disable (default: 90) +- `--cachedir` — cache dir holding pre-built `conda/` and `singularity/` subdirs (default: `~/.bactopia`; use `/data/cache` on this host) +- `--generate` — force regeneration of the docker snapshot, overwriting the committed `.snap` (default: off; a missing snapshot is generated regardless) +- `--force-rebuild` — force a rebuild of existing Conda envs and Singularity images (default: off) +- `--max-retry` — max build retries per environment during the build phase (default: 3) +- `--jobs` — components tested in parallel; the 4 profiles within a component run sequentially (default: 32) +- `--fail-fast` — stop on the first component with any failing profile (default: off) +- `--timeout` — per-run timeout in **minutes** (kills each nf-test subprocess), 0 to disable (default: 90) +- `--times` — path to test-times baseline JSON; enables per-component timeouts and longest-first ordering (default: `{bactopia-path}/conf/test-times.json`) +- `--timeout-multiplier` / `-tm` — per-component timeout = `min(expected_seconds * this, --timeout)`; only applied when a test-times file is available (default: 4) **Cleanup (operates instead of running tests)** - `--cleanup` — remove `.nf-test/` temp files under `modules/`, `subworkflows/`, `workflows/`, `tests/`, then exit (skips `logs/` work dirs) @@ -214,7 +252,6 @@ Defaults in parentheses. **Output** - `--outdir` — directory to write `logs/` into (default: `.`) -- `--keep` — preserve `.nf-test/` dirs and logs on pass (default: off) - `--json` — emit results as JSON (default: off; used only as fallback) **Logging** @@ -222,24 +259,36 @@ Defaults in parentheses. - `--silent` — ERROR logging only - `--version` / `--help` +> Removed in the suite revamp: `--profile`, `--condadir`, `--singularity_cache` +> (folded into the 4-profile matrix + `--cachedir`), and `--keep` (per-profile +> logs and `.nf-test/` work dirs are now always preserved under `logs/`). + ### Output layout written by the CLI ``` {outdir}/logs/run-tests/{YYYYMMDD_HHMMSS}/ -├── summary.json # machine-readable rollup -├── summary.tsv # same data in TSV +├── summary.json # machine-readable rollup (first line of .tsv is `# generate=`) +├── summary.tsv # same data in TSV ├── modules/ -│ ├── {component}.stdout.txt # captured stdout from nf-test -│ ├── {component}.stderr.txt # captured stderr -│ └── {component}.outputs.txt # undeclared-outputs report +│ └── {component}/ +│ ├── docker/ # one dir per profile that ran +│ │ ├── stdout.txt # nf-test console incl. tool `Command error:` block +│ │ ├── stderr.txt # nf-test assertions / `Different Snapshot` md5 diff +│ │ ├── outputs.txt # undeclared-outputs report (or `# OK`) +│ │ └── .nf-test/ # preserved work tree (all cells, passing included) +│ ├── conda/ ... +│ ├── singularity_galaxy/ ... +│ └── singularity_pull/ ... ├── subworkflows/ │ └── ... (same structure) └── workflows/ └── ... (same structure) ``` -Only the tiers that were tested have subdirectories in a given run. -`/review-tests` reads these files directly -- do not pre-load them here. +Only the tiers that were tested have subdirectories in a given run, and a +component only has a `{profile}/` dir for each profile that actually ran (a +component with no Galaxy image has no `singularity_galaxy/`). `/review-tests` +reads these files directly -- do not pre-load them here. ### Wrapper script discovery order @@ -276,4 +325,4 @@ are forwarded through `"$@"`. loop but uses the same wrapper-script pattern. - `/update-module` — bumps tool versions. Unrelated, but is the reference for the "ask the user before mutating" pattern borrowed here for - `--generate` and profile switches. + `--generate` and `--force-rebuild`. From da0c725016be2e7662b8dbea1ace5a592bf9454b Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 19:37:36 -0600 Subject: [PATCH 37/43] update bactopia-py pinning --- data/conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml index 5fcfddf62..175445ad1 100644 --- a/data/conda/meta.yaml +++ b/data/conda/meta.yaml @@ -17,7 +17,7 @@ requirements: - python >3.9,<3.14 - wget run: - - bactopia-py >=2.4.0 + - bactopia-py >=2.4.2 - conda >=25 - coreutils - mamba >=2 From 2c048ec1a04c5235930385116a176edd25651d95 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 21:27:02 -0600 Subject: [PATCH 38/43] add sample samples to ariba outputs --- .agents/docs/standards/03-technical-specs.md | 2 +- CHANGELOG.md | 5 ++++- catalog.json | 4 ++-- modules/ariba/run/main.nf | 4 ++++ modules/ariba/run/tests/main.nf.test.snap | 6 +++--- subworkflows/ariba/tests/main.nf.test.snap | 2 +- workflows/bactopia-tools/ariba/tests/main.nf.test.snap | 10 +++++----- 7 files changed, 20 insertions(+), 13 deletions(-) diff --git a/.agents/docs/standards/03-technical-specs.md b/.agents/docs/standards/03-technical-specs.md index 59afa263e..375b282e8 100644 --- a/.agents/docs/standards/03-technical-specs.md +++ b/.agents/docs/standards/03-technical-specs.md @@ -509,7 +509,7 @@ GATHER is the only module that appends a `*???-` suffix — it runs before Many tools do not accept gzip-compressed input (or cannot follow symlinks). Since assemblies and other inputs may arrive either compressed (`.gz`) or plain, modules that need a real file -on disk use a standard decompress-or-copy guard. This is the convention used across ~34 modules +on disk use a standard decompress-or-copy guard. This is the convention used across roughly three dozen modules (e.g., `agrvate`, `ectyper`, `mobsuite/recon`, `checkm2/predict`, `clonalframeml`). In the Groovy script block, before the shell heredoc: diff --git a/CHANGELOG.md b/CHANGELOG.md index f94f48a3e..fe8a0aec9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,10 @@ sidebar_position: 5000 # Changelog -## v4.1.0 bactopia/bactopia "???" 2026/??/?? +## v4.1.0 bactopia/bactopia "Cheyenne Frontier Days" 2026/08/04 + + +_"[Cheyenne Frontier Days (CFD)](https://cfdrodeo.com/)" ten days of rodeos, music, and carnival rides_ ### `Added` diff --git a/catalog.json b/catalog.json index 3751824de..0becbb436 100644 --- a/catalog.json +++ b/catalog.json @@ -1,8 +1,8 @@ { "version": "1.0", - "generated": "2026-08-04T18:35:56Z", + "generated": "2026-08-05T02:01:25Z", "bactopia_version": "4.1.0", - "bactopia_py_version": "2.3.0", + "bactopia_py_version": "2.4.2", "nf_bactopia_version": "2.1.7", "modules": { "abricate_run": { diff --git a/modules/ariba/run/main.nf b/modules/ariba/run/main.nf index c758a7502..23287b5db 100644 --- a/modules/ariba/run/main.nf +++ b/modules/ariba/run/main.nf @@ -104,6 +104,10 @@ process ARIBA_RUN { mv ${db_name}/summary.csv ./${prefix}-summary.csv mv ${db_name}/ supplemental/ + # Prepend a sample column so merged results can be traced to the sample + sed -i -e '1s|^name|sample,database|' -e '1!s|^|${prefix},|' ${prefix}-summary.csv + sed -i -e '1s|^#ariba_ref_name|sample\tariba_ref_name|' -e '1!s|^|${prefix}\t|' ${prefix}-report.tsv + # Cleanup rm -rf ${db_name}db diff --git a/modules/ariba/run/tests/main.nf.test.snap b/modules/ariba/run/tests/main.nf.test.snap index b4acf088a..7a11e1e8c 100644 --- a/modules/ariba/run/tests/main.nf.test.snap +++ b/modules/ariba/run/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "process_name": "ariba", "scope": "sample" }, - "SRR2838702-report.tsv:md5,5ee10dd85eb51e673a8eb7e07298c69d", - "SRR2838702-summary.csv:md5,e973fbf0fffdcfc500bfba85549239e4", + "SRR2838702-report.tsv:md5,a7574299aadfff54270d5f7657ad5d54", + "SRR2838702-summary.csv:md5,39cbff7dcb0c255ea78dc6d9bfc19749", [ "versions.yml:md5,2d20a87ab1578332cae79c947a52e8f8" ] ], - "timestamp": "2026-07-30T19:01:48.501156944", + "timestamp": "2026-08-04T21:00:57.091217972", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/subworkflows/ariba/tests/main.nf.test.snap b/subworkflows/ariba/tests/main.nf.test.snap index 543928172..ef161881c 100644 --- a/subworkflows/ariba/tests/main.nf.test.snap +++ b/subworkflows/ariba/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6" ] ], - "timestamp": "2026-07-30T19:12:08.845212811", + "timestamp": "2026-08-04T21:04:45.138370394", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap index 3b4e5ada0..925c4df52 100644 --- a/workflows/bactopia-tools/ariba/tests/main.nf.test.snap +++ b/workflows/bactopia-tools/ariba/tests/main.nf.test.snap @@ -56,16 +56,16 @@ "bactopia-runs/ariba-card/nf-reports/ariba-timeline.html" ], [ - "SRR2838702-report.tsv:md5,3d4492a0da3197a00e7a5da818e4c1ea", - "SRR2838702-summary.csv:md5,b6735bd13bad29a22a5c99fcabb1959f", + "SRR2838702-report.tsv:md5,963488ef79fccc1a281498f4700c2250", + "SRR2838702-summary.csv:md5,c61c9e5e1534314b727333f7fbd31571", "versions.yml:md5,aaa688e30363067240a27dcbe85f29c6", - "card-report.tsv:md5,3d4492a0da3197a00e7a5da818e4c1ea", - "card-summary.csv:md5,b6735bd13bad29a22a5c99fcabb1959f", + "card-report.tsv:md5,963488ef79fccc1a281498f4700c2250", + "card-summary.csv:md5,c61c9e5e1534314b727333f7fbd31571", "versions.yml:md5,ff3a06461ce07f813e0b9e2739bb05ca", "versions.yml:md5,1a4d97856cb563f9b6c84132cd60d481" ] ], - "timestamp": "2026-07-30T19:16:56.885968394", + "timestamp": "2026-08-04T21:01:00.564375661", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 79b9f82e8f7aa88d8bef0cf9a3e09de57c292cd1 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 21:27:50 -0600 Subject: [PATCH 39/43] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe8a0aec9..59062aad5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -88,6 +88,7 @@ _"[Cheyenne Frontier Days (CFD)](https://cfdrodeo.com/)" ten days of rodeos, mus - `mcroni` - `numpy=2.0` (`reshape(newshape=)` removed in NumPy 2.1) - `clermontyping` - `r-readr=2.1` (`quoted_na` promoted to a hard error) - `snippy` (bactopia-variants) - `htslib=1.14` (bcftools 1.14/htslib 1.21 ABI mismatch segfaulted `bcftools consensus`) +- added sample samples to ariba outputs ## v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29 From a7b7a24fab37a77270953bb7af08d8cc40f147d7 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 21:58:03 -0600 Subject: [PATCH 40/43] update schemas missing default boolean values --- modules/ariba/run/schema.json | 1 + modules/bactopia/assembler/schema.json | 4 ++++ modules/bactopia/gather/schema.json | 2 ++ modules/bactopia/qc/schema.json | 4 ++++ modules/bactopia/sketcher/schema.json | 1 + modules/defensefinder/run/schema.json | 2 ++ modules/eggnog/download/schema.json | 5 +++-- nextflow_schema.json | 11 +++++++++++ workflows/bactopia-tools/ariba/nextflow_schema.json | 1 + .../bactopia-tools/defensefinder/nextflow_schema.json | 2 ++ workflows/bactopia-tools/eggnog/nextflow_schema.json | 5 +++-- workflows/cleanyerreads/nextflow_schema.json | 6 ++++++ workflows/staphopia/nextflow_schema.json | 11 +++++++++++ workflows/teton/nextflow_schema.json | 2 ++ 14 files changed, 53 insertions(+), 4 deletions(-) diff --git a/modules/ariba/run/schema.json b/modules/ariba/run/schema.json index 749eb1540..955d51ebd 100644 --- a/modules/ariba/run/schema.json +++ b/modules/ariba/run/schema.json @@ -92,6 +92,7 @@ }, "ariba_no_clean": { "type": "boolean", + "default": false, "description": "Do not clean up intermediate files created by Ariba.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/modules/bactopia/assembler/schema.json b/modules/bactopia/assembler/schema.json index 19c64d536..9bff9c8b2 100644 --- a/modules/bactopia/assembler/schema.json +++ b/modules/bactopia/assembler/schema.json @@ -39,6 +39,7 @@ }, "use_unicycler": { "type": "boolean", + "default": false, "description": "Use unicycler for paired end assembly", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -159,18 +160,21 @@ }, "no_polish": { "type": "boolean", + "default": false, "description": "Skip the assembly polishing step", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_miniasm": { "type": "boolean", + "default": false, "description": "Skip miniasm+Racon bridging", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_rotate": { "type": "boolean", + "default": false, "description": "Do not rotate completed replicons to start at a standard gene", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/modules/bactopia/gather/schema.json b/modules/bactopia/gather/schema.json index dffaf2836..47f65e5f5 100644 --- a/modules/bactopia/gather/schema.json +++ b/modules/bactopia/gather/schema.json @@ -14,6 +14,7 @@ "properties": { "skip_fastq_check": { "type": "boolean", + "default": false, "description": "Skip minimum requirement checks for input FASTQs", "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.", "fa_icon": "fas fa-toggle-on", @@ -71,6 +72,7 @@ }, "use_ena": { "type": "boolean", + "default": false, "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/modules/bactopia/qc/schema.json b/modules/bactopia/qc/schema.json index d07ae13b1..545f625db 100644 --- a/modules/bactopia/qc/schema.json +++ b/modules/bactopia/qc/schema.json @@ -14,6 +14,7 @@ "properties": { "use_bbmap": { "type": "boolean", + "default": false, "description": "Illumina reads will be QC'd using BBMap", "help": "", "fa_icon": "fas fa-toggle-on", @@ -29,6 +30,7 @@ }, "skip_qc": { "type": "boolean", + "default": false, "description": "The QC step will be skipped and it will be assumed the inputs sequences have already been QCed.", "help": "This is really only useful if you have already QC'd your reads, or have a specific need", "fa_icon": "fas fa-toggle-on", @@ -36,12 +38,14 @@ }, "skip_qc_plots": { "type": "boolean", + "default": false, "description": "QC Plot creation by FastQC or Nanoplot will be skipped", "fa_icon": "fas fa-toggle-on", "hidden": true }, "skip_error_correction": { "type": "boolean", + "default": false, "description": "FLASH error correction of reads will be skipped.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/modules/bactopia/sketcher/schema.json b/modules/bactopia/sketcher/schema.json index 16f74dca1..d35cde8ea 100644 --- a/modules/bactopia/sketcher/schema.json +++ b/modules/bactopia/sketcher/schema.json @@ -28,6 +28,7 @@ }, "no_winner_take_all": { "type": "boolean", + "default": false, "description": "Disable winner-takes-all strategy for identity estimates", "help": "winner-take-all description: After counting hashes for each query, hashes that appear in multiple queries will be removed from all except the one with the best identity (ties broken by larger query), and other identities will be reduced. This removes output redundancy, providing a rough compositional outline.", "fa_icon": "fas fa-toggle-on", diff --git a/modules/defensefinder/run/schema.json b/modules/defensefinder/run/schema.json index e0c704472..51e6cf260 100644 --- a/modules/defensefinder/run/schema.json +++ b/modules/defensefinder/run/schema.json @@ -31,12 +31,14 @@ }, "defensefinder_preserveraw": { "type": "boolean", + "default": false, "description": "Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory", "fa_icon": "fas fa-toggle-on", "hidden": true }, "defensefinder_nocutga": { "type": "boolean", + "default": false, "description": "Advanced! Run macsyfinder in no-cut-ga mode. The validity of the genes and systems found is not guaranteed!", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/modules/eggnog/download/schema.json b/modules/eggnog/download/schema.json index 343fcb3d5..03f351ace 100644 --- a/modules/eggnog/download/schema.json +++ b/modules/eggnog/download/schema.json @@ -25,9 +25,10 @@ "fa_icon": "fas fa-toggle-on" }, "eggnog_save_as_tarball": { - "type": "string", + "type": "boolean", + "default": false, "description": "Save the eggNOG database as a single tarball", - "fa_icon": "fas fa-font" + "fa_icon": "fas fa-toggle-on" }, "eggnog_skip_diamond": { "type": "boolean", diff --git a/nextflow_schema.json b/nextflow_schema.json index 870ff8086..96336430d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -244,6 +244,7 @@ }, "use_unicycler": { "type": "boolean", + "default": false, "description": "Use unicycler for paired end assembly", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -364,18 +365,21 @@ }, "no_polish": { "type": "boolean", + "default": false, "description": "Skip the assembly polishing step", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_miniasm": { "type": "boolean", + "default": false, "description": "Skip miniasm+Racon bridging", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_rotate": { "type": "boolean", + "default": false, "description": "Do not rotate completed replicons to start at a standard gene", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -412,6 +416,7 @@ "properties": { "skip_fastq_check": { "type": "boolean", + "default": false, "description": "Skip minimum requirement checks for input FASTQs", "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.", "fa_icon": "fas fa-toggle-on", @@ -469,6 +474,7 @@ }, "use_ena": { "type": "boolean", + "default": false, "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -498,6 +504,7 @@ }, "no_winner_take_all": { "type": "boolean", + "default": false, "description": "Disable winner-takes-all strategy for identity estimates", "help": "winner-take-all description: After counting hashes for each query, hashes that appear in multiple queries will be removed from all except the one with the best identity (ties broken by larger query), and other identities will be reduced. This removes output redundancy, providing a rough compositional outline.", "fa_icon": "fas fa-toggle-on", @@ -572,6 +579,7 @@ "properties": { "use_bbmap": { "type": "boolean", + "default": false, "description": "Illumina reads will be QC'd using BBMap", "help": "", "fa_icon": "fas fa-toggle-on", @@ -587,6 +595,7 @@ }, "skip_qc": { "type": "boolean", + "default": false, "description": "The QC step will be skipped and it will be assumed the inputs sequences have already been QCed.", "help": "This is really only useful if you have already QC'd your reads, or have a specific need", "fa_icon": "fas fa-toggle-on", @@ -594,12 +603,14 @@ }, "skip_qc_plots": { "type": "boolean", + "default": false, "description": "QC Plot creation by FastQC or Nanoplot will be skipped", "fa_icon": "fas fa-toggle-on", "hidden": true }, "skip_error_correction": { "type": "boolean", + "default": false, "description": "FLASH error correction of reads will be skipped.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/workflows/bactopia-tools/ariba/nextflow_schema.json b/workflows/bactopia-tools/ariba/nextflow_schema.json index 53abce65f..2caa42dd0 100644 --- a/workflows/bactopia-tools/ariba/nextflow_schema.json +++ b/workflows/bactopia-tools/ariba/nextflow_schema.json @@ -129,6 +129,7 @@ }, "ariba_no_clean": { "type": "boolean", + "default": false, "description": "Do not clean up intermediate files created by Ariba.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/workflows/bactopia-tools/defensefinder/nextflow_schema.json b/workflows/bactopia-tools/defensefinder/nextflow_schema.json index 7da2d41b5..d5e674aa1 100644 --- a/workflows/bactopia-tools/defensefinder/nextflow_schema.json +++ b/workflows/bactopia-tools/defensefinder/nextflow_schema.json @@ -68,12 +68,14 @@ }, "defensefinder_preserveraw": { "type": "boolean", + "default": false, "description": "Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory", "fa_icon": "fas fa-toggle-on", "hidden": true }, "defensefinder_nocutga": { "type": "boolean", + "default": false, "description": "Advanced! Run macsyfinder in no-cut-ga mode. The validity of the genes and systems found is not guaranteed!", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/workflows/bactopia-tools/eggnog/nextflow_schema.json b/workflows/bactopia-tools/eggnog/nextflow_schema.json index fdde4cdd5..06f135ef3 100644 --- a/workflows/bactopia-tools/eggnog/nextflow_schema.json +++ b/workflows/bactopia-tools/eggnog/nextflow_schema.json @@ -62,9 +62,10 @@ "fa_icon": "fas fa-toggle-on" }, "eggnog_save_as_tarball": { - "type": "string", + "type": "boolean", + "default": false, "description": "Save the eggNOG database as a single tarball", - "fa_icon": "fas fa-font" + "fa_icon": "fas fa-toggle-on" }, "eggnog_skip_diamond": { "type": "boolean", diff --git a/workflows/cleanyerreads/nextflow_schema.json b/workflows/cleanyerreads/nextflow_schema.json index 0b45d78bd..51e466d46 100644 --- a/workflows/cleanyerreads/nextflow_schema.json +++ b/workflows/cleanyerreads/nextflow_schema.json @@ -78,6 +78,7 @@ "properties": { "skip_fastq_check": { "type": "boolean", + "default": false, "description": "Skip minimum requirement checks for input FASTQs", "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.", "fa_icon": "fas fa-toggle-on", @@ -135,6 +136,7 @@ }, "use_ena": { "type": "boolean", + "default": false, "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -166,6 +168,7 @@ "properties": { "use_bbmap": { "type": "boolean", + "default": false, "description": "Illumina reads will be QC'd using BBMap", "help": "", "fa_icon": "fas fa-toggle-on", @@ -181,6 +184,7 @@ }, "skip_qc": { "type": "boolean", + "default": false, "description": "The QC step will be skipped and it will be assumed the inputs sequences have already been QCed.", "help": "This is really only useful if you have already QC'd your reads, or have a specific need", "fa_icon": "fas fa-toggle-on", @@ -188,12 +192,14 @@ }, "skip_qc_plots": { "type": "boolean", + "default": false, "description": "QC Plot creation by FastQC or Nanoplot will be skipped", "fa_icon": "fas fa-toggle-on", "hidden": true }, "skip_error_correction": { "type": "boolean", + "default": false, "description": "FLASH error correction of reads will be skipped.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/workflows/staphopia/nextflow_schema.json b/workflows/staphopia/nextflow_schema.json index 711c74d2f..d5ac57090 100644 --- a/workflows/staphopia/nextflow_schema.json +++ b/workflows/staphopia/nextflow_schema.json @@ -239,6 +239,7 @@ }, "use_unicycler": { "type": "boolean", + "default": false, "description": "Use unicycler for paired end assembly", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -359,18 +360,21 @@ }, "no_polish": { "type": "boolean", + "default": false, "description": "Skip the assembly polishing step", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_miniasm": { "type": "boolean", + "default": false, "description": "Skip miniasm+Racon bridging", "fa_icon": "fas fa-toggle-on", "hidden": true }, "no_rotate": { "type": "boolean", + "default": false, "description": "Do not rotate completed replicons to start at a standard gene", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -407,6 +411,7 @@ "properties": { "skip_fastq_check": { "type": "boolean", + "default": false, "description": "Skip minimum requirement checks for input FASTQs", "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.", "fa_icon": "fas fa-toggle-on", @@ -464,6 +469,7 @@ }, "use_ena": { "type": "boolean", + "default": false, "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true @@ -493,6 +499,7 @@ }, "no_winner_take_all": { "type": "boolean", + "default": false, "description": "Disable winner-takes-all strategy for identity estimates", "help": "winner-take-all description: After counting hashes for each query, hashes that appear in multiple queries will be removed from all except the one with the best identity (ties broken by larger query), and other identities will be reduced. This removes output redundancy, providing a rough compositional outline.", "fa_icon": "fas fa-toggle-on", @@ -567,6 +574,7 @@ "properties": { "use_bbmap": { "type": "boolean", + "default": false, "description": "Illumina reads will be QC'd using BBMap", "help": "", "fa_icon": "fas fa-toggle-on", @@ -582,6 +590,7 @@ }, "skip_qc": { "type": "boolean", + "default": false, "description": "The QC step will be skipped and it will be assumed the inputs sequences have already been QCed.", "help": "This is really only useful if you have already QC'd your reads, or have a specific need", "fa_icon": "fas fa-toggle-on", @@ -589,12 +598,14 @@ }, "skip_qc_plots": { "type": "boolean", + "default": false, "description": "QC Plot creation by FastQC or Nanoplot will be skipped", "fa_icon": "fas fa-toggle-on", "hidden": true }, "skip_error_correction": { "type": "boolean", + "default": false, "description": "FLASH error correction of reads will be skipped.", "fa_icon": "fas fa-toggle-on", "hidden": true diff --git a/workflows/teton/nextflow_schema.json b/workflows/teton/nextflow_schema.json index 4b9af5a0c..30efd0517 100644 --- a/workflows/teton/nextflow_schema.json +++ b/workflows/teton/nextflow_schema.json @@ -78,6 +78,7 @@ "properties": { "skip_fastq_check": { "type": "boolean", + "default": false, "description": "Skip minimum requirement checks for input FASTQs", "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.", "fa_icon": "fas fa-toggle-on", @@ -135,6 +136,7 @@ }, "use_ena": { "type": "boolean", + "default": false, "description": "Download FASTQs from ENA", "fa_icon": "fas fa-toggle-on", "hidden": true From 8336263784dd10dc5d09b1382054a1e0396f436b Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 22:28:14 -0600 Subject: [PATCH 41/43] fix yaml frontmatter in update-datasets skill --- .agents/skills/update-datasets/SKILL.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.agents/skills/update-datasets/SKILL.md b/.agents/skills/update-datasets/SKILL.md index 93a9e2dc7..765db136b 100644 --- a/.agents/skills/update-datasets/SKILL.md +++ b/.agents/skills/update-datasets/SKILL.md @@ -1,6 +1,6 @@ --- name: update-datasets -description: Build and publish Bactopia's version-pinned datasets to Cloudflare R2. Currently implements the AMRFinder+ database: verifies the amrfinderplus module is at the latest bioconda version, rebuilds amrfinderplus.tar.gz inside the module's pinned container, and (after confirmation) uploads it via rclone to datasets/v/amrfinderplus.tar.gz. Use when asked to update datasets, rebuild the amrfinderplus database, publish a dataset bundle, refresh the version-pinned datasets, or prepare datasets for a release. +description: Build and publish Bactopia's version-pinned datasets to Cloudflare R2. Currently implements the AMRFinder+ database. It verifies the amrfinderplus module is at the latest bioconda version, rebuilds amrfinderplus.tar.gz inside the module's pinned container, and (after confirmation) uploads it via rclone to datasets/v/amrfinderplus.tar.gz. Use when asked to update datasets, rebuild the amrfinderplus database, publish a dataset bundle, refresh the version-pinned datasets, or prepare datasets for a release. --- # Update Datasets From e299400259ef9321e6325040a2feb1aa965fa748 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 4 Aug 2026 22:50:02 -0600 Subject: [PATCH 42/43] lets not release at 11pm -.-, save it for tomorrow! --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 59062aad5..e42951420 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ sidebar_position: 5000 # Changelog -## v4.1.0 bactopia/bactopia "Cheyenne Frontier Days" 2026/08/04 +## v4.1.0 bactopia/bactopia "Cheyenne Frontier Days" 2026/08/05 _"[Cheyenne Frontier Days (CFD)](https://cfdrodeo.com/)" ten days of rodeos, music, and carnival rides_ From f0ec476468a30a04af5cf5eb90d13d8d8284aed6 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 5 Aug 2026 07:56:30 -0600 Subject: [PATCH 43/43] update changelog --- CHANGELOG.md | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e42951420..ad891d1b3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,12 +22,11 @@ _"[Cheyenne Frontier Days (CFD)](https://cfdrodeo.com/)" ten days of rodeos, mus - Deacon as the default host read scrubber (replaces nohuman as default) - Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules - Three-way scrubber selection: deacon (default), nohuman (`--use_nohuman`), SRA Human Scrubber (`--use_srascrubber`) -- `genomedl` module and subworkflow - download genome assemblies from NCBI Datasets with `genome-dl` +- `genomedl` module and subworkflow - download assemblies from NCBI Datasets with `genome-dl` - resolves version-less accessions to the latest assembly version - subsamples `--species` downloads with `--limit` instead of `shuf | head` - - `--limit` defaults to 100 to prevent accidentally downloading 50k+ genomes (`--limit 0` for no limit) - - subworkflow emits `assemblies` from the named `fna` field, and `reference` from `gbff` when - `--format genbank` is used (Snippy needs an annotated reference), otherwise `fna` + - `--limit` defaults to 100 to prevent downloading 50k+ genomes (`--limit 0` for no limit) + - subworkflow emits `assemblies` from the named `fna` field, and `reference` from `gbff` - Bump internal bactopia-* pipeline tool versions - `bactopia-gather`: 1.0.5 -> 1.2.0 - bump program versions in modules @@ -55,33 +54,33 @@ _"[Cheyenne Frontier Days (CFD)](https://cfdrodeo.com/)" ten days of rodeos, mus `genomedl` instead of `ncbigenomedownload` - `--kingdom` and `--keep_downloads` are no longer available to these tools - `--limit` now defaults to 100 for `--species` (previously unlimited) - - `snippy --accession` requires `--format genbank`, since Snippy needs an annotated reference + - `snippy --accession` requires `--format genbank` for an annotated reference - Deacon modules now use bactopia-teton container instead of standalone deacon container - Teton and scrubber workflows default to deacon instead of nohuman for host read removal - cleanyerreads workflow supports `--use_deacon` flag for host read removal -- Added `params.bactopia_dir` which anchors to the Bactopia repo root so `data/` can be reference by all workflows -- Centralized the pipeline version and `nf-bactopia@` plugin pin for module/subworkflow tests into `conf/test_base.config`; each `tests/nextflow.config` now `includeConfig`s it instead of repeating the values, so a version bump touches one file -- Migrated AI agent context to the community-standard layout: `CLAUDE.md` is now `AGENTS.md` (agents.md convention, read natively by omp/pi, Kimi Code, Codex, Cursor, and others), and `.claude/docs` + `.claude/skills` moved to `.agents/docs` + `.agents/skills` - - Claude Code compatibility is preserved via a one-line `CLAUDE.md` shim (`@AGENTS.md`) and a `.claude/skills` symlink - - `llms.txt` template updated: module layout corrected (`module.config`/`schema.json`, not `meta.yml`) and the full `.agents/docs/` index is now listed +- Added `params.bactopia_dir` (repo root) so `data/` can be referenced by all workflows +- Centralized configuration for module/subworkflow tests into `conf/test_base.config` +- Transitioned LLM context to be provider agnostic + - `CLAUDE.md` is now `AGENTS.md` following agents.md standard + - `.claude/docs` and `.claude/skills` moved to `.agents/docs` + `.agents/skills` + - Preserved Claude Code compatibility via `CLAUDE.md` shim and symlinks in `.claude/skills` + - `llms.txt` and `catalog.json` updated with latest changes ### `Fixed` - float parameters being interpreted as strings in CLI - `--prokka_proteins` not being found in non-Bactopia workflows - `--fastani_skip_pairwise` parameter that does not exist -- `mlst` and `amrfinderplus` Bactopia Tools failing immediately with `ERROR ~ Path string cannot - be empty` when run without `--mlst_db` / `--amrfinderplus_db` ([#673](https://github.com/bactopia/bactopia/issues/673)) +- `mlst` and `amrfinderplus` Bactopia Tools failing with `ERROR ~ Path string cannot be empty` - `mlst` Bactopia Tool not falling back on bactopia/datasets - `mobsuite` failing on any sample without plasmids due to compressing non-existent files - removed unused `amrfinderplus/update` module -- `rgi` failing with `unrecognized arguments: --num_threads` after the 6.0.8 bump (renamed to `--threads`) -- `rgi_exclude_nudge` emitting the removed `--exclude_nudge` flag; replaced with `rgi_include_nudge` which passes RGI 6's opt-in `--include_nudge` -- `bactopia datasets` tests requesting a version-pinned `mlst.tar.gz` (404); `mlst_url` has been version-less since v4.0.0 +- `rgi` failing with `unrecognized arguments: --num_threads` (renamed to `--threads`) +- `rgi_exclude_nudge` replaced with `rgi_include_nudge` +- `bactopia datasets` tests requesting a version-pinned `mlst.tar.gz` (404) - `gubbins` failing under Singularity/Apptainer when Numba tried to write to read-only container ([#667](https://github.com/bactopia/bactopia/issues/667)) (@pvanheus) - `agrvate`, `gamma`, and `traitar` modules failing under Conda with `cp: '...' are the same file` - when the staged input was copied onto its own path (used `fna.fileName.name` for the work-dir copy target) -- Conda profile tool_errors from unconstrained transitive dependencies (docker/singularity unaffected); pinned in each module's `ext.toolName`: +- Conda errors due to loose pinnings - `ariba`, `ismapper`, `mykrobe`, `shigeifinder`, `sistr` - `setuptools=80` (`pkg_resources` removed in setuptools 81) - `clonalframeml` (maskrc-svg) - `python=3.12` (stdlib `cgi` removed in Python 3.13) - `hicap` - `biopython=1.79` (`SeqFeature.strand` removed in Biopython 1.80)