From 01c289648f98284e86c30fd5c4ec4fb101ad57a4 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 28 Jan 2026 18:03:12 +0000 Subject: [PATCH 1/6] Convert untar, pigz/compress, kallisto/index, samtools/index, bowtie2/build to topic-based version emission Converts these modules from versions.yml file emission to the modern topic: versions channel emission pattern. Changes per module: - main.nf: Replace `path "versions.yml", emit: versions` with `tuple val("${task.process}"), val(''), eval(''), emit: versions_, topic: versions` - main.nf: Remove heredoc version blocks from script and stub sections - meta.yml: Remove old versions output, add versions_ output and topics section - tests: Update assertions to use findAll for versions outputs - tests: Regenerate snapshots with structured version tuples Updates 11 subworkflows to remove explicit version collection for converted modules (versions now collected via topic channel): - archive_extract - bam_sort_stats_samtools - bam_dedup_stats_samtools_umitools - bam_markduplicates_picard - bam_dedup_stats_samtools_umicollapse - fastq_align_bwaaln - bam_split_by_region - fastq_remove_rrna - fasta_index_dna - fasta_index_bismark_bwameth - fasta_index_methylseq Co-Authored-By: Claude Opus 4.5 --- modules/nf-core/bowtie2/build/main.nf | 11 +- modules/nf-core/bowtie2/build/meta.yml | 84 +++--- .../nf-core/bowtie2/build/tests/main.nf.test | 9 +- .../bowtie2/build/tests/main.nf.test.snap | 56 ++-- modules/nf-core/kallisto/index/main.nf | 12 +- modules/nf-core/kallisto/index/meta.yml | 34 ++- .../nf-core/kallisto/index/tests/main.nf.test | 7 +- .../kallisto/index/tests/main.nf.test.snap | 59 ++-- modules/nf-core/pigz/compress/main.nf | 12 +- modules/nf-core/pigz/compress/meta.yml | 29 +- .../nf-core/pigz/compress/tests/main.nf.test | 10 +- .../pigz/compress/tests/main.nf.test.snap | 55 ++-- modules/nf-core/samtools/index/main.nf | 12 +- modules/nf-core/samtools/index/meta.yml | 28 +- .../nf-core/samtools/index/tests/main.nf.test | 27 +- .../samtools/index/tests/main.nf.test.snap | 278 ++++++------------ modules/nf-core/untar/main.nf | 11 +- modules/nf-core/untar/meta.yml | 28 +- modules/nf-core/untar/tests/main.nf.test | 20 +- modules/nf-core/untar/tests/main.nf.test.snap | 176 +++++------ subworkflows/nf-core/archive_extract/main.nf | 1 - .../archive_extract/tests/main.nf.test.snap | 4 +- .../main.nf | 1 - .../tests/main.nf.test.snap | 7 +- .../bam_dedup_stats_samtools_umitools/main.nf | 1 - .../tests/main.nf.test.snap | 15 +- .../nf-core/bam_markduplicates_picard/main.nf | 1 - .../tests/main.nf.test.snap | 22 +- .../nf-core/bam_sort_stats_samtools/main.nf | 1 - .../tests/main.nf.test.snap | 22 +- .../nf-core/bam_split_by_region/main.nf | 1 - .../tests/main.nf.test.snap | 16 +- .../fasta_index_bismark_bwameth/main.nf | 2 - .../tests/main.nf.test.snap | 36 +-- subworkflows/nf-core/fasta_index_dna/main.nf | 1 - .../fasta_index_dna/tests/main.nf.test.snap | 32 +- .../nf-core/fasta_index_methylseq/main.nf | 3 - .../tests/main.nf.test.snap | 36 +-- .../nf-core/fastq_align_bwaaln/main.nf | 1 - .../tests/main.nf.test.snap | 28 +- .../nf-core/fastq_remove_rrna/main.nf | 1 - .../fastq_remove_rrna/tests/main.nf.test.snap | 9 +- 42 files changed, 534 insertions(+), 665 deletions(-) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index fb7effec4a4a..1be06ac89d77 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -12,7 +12,7 @@ process BOWTIE2_BUILD { output: tuple val(meta), path('bowtie2') , emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bowtie2'), eval('bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"'), emit: versions_bowtie2, topic: versions when: task.ext.when == null || task.ext.when @@ -22,10 +22,6 @@ process BOWTIE2_BUILD { """ mkdir bowtie2 bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') - END_VERSIONS """ stub: @@ -33,10 +29,5 @@ process BOWTIE2_BUILD { mkdir bowtie2 touch bowtie2/${fasta.baseName}.{1..4}.bt2 touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 3e83ecb42e4f..6e0401e4976c 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -1,31 +1,31 @@ name: bowtie2_build description: Builds bowtie index for reference genome keywords: - - build - - index - - fasta - - genome - - reference +- build +- index +- fasta +- genome +- reference tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ["GPL-3.0-or-later"] - identifier: "" +- bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] + identifier: "" input: - - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - ontologies: [] +- - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + ontologies: [] output: index: - - meta: @@ -34,20 +34,36 @@ output: Groovy Map containing reference information e.g. [ id:'test', single_end:false ] - bowtie2: - type: file + type: directory description: Bowtie2 genome index files pattern: "*.bt2" ontologies: [] + versions_bowtie2: + - - ${task.process}: + type: string + description: The name of the process + - bowtie2: + type: string + description: The name of the tool + - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"': + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - bowtie2: + type: string + description: The name of the tool + - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"': + type: eval + description: The expression to obtain the version of the tool + authors: - - "@joseespinosa" - - "@drpatelh" +- "@joseespinosa" +- "@drpatelh" maintainers: - - "@joseespinosa" - - "@drpatelh" +- "@joseespinosa" +- "@drpatelh" diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test index ee94c19c911c..a4bad2a10f75 100644 --- a/modules/nf-core/bowtie2/build/tests/main.nf.test +++ b/modules/nf-core/bowtie2/build/tests/main.nf.test @@ -22,8 +22,13 @@ nextflow_process { } then { - assert process.success - assert snapshot(process.out).match() + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.index, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) } } diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap index ea5711e42668..9f1bf08038de 100644 --- a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap +++ b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap @@ -1,49 +1,35 @@ { "Should run without failures": { "content": [ - { - "0": [ + [ + [ + { + "id": "test" + }, [ - { - "id": "test" - }, - [ - "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", - "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", - "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" - ] + "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", + "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", + "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" ] - ], - "1": [ - "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c" - ], - "index": [ + ] + ], + { + "versions_bowtie2": [ [ - { - "id": "test" - }, - [ - "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", - "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", - "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" - ] + "BOWTIE2_BUILD", + "bowtie2", + "2.5.4" ] - ], - "versions": [ - "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.02.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2023-11-23T11:51:01.107681997" + "timestamp": "2026-01-28T17:52:30.165111" } } \ No newline at end of file diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 73a5f7a951ec..5174924eb706 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -12,7 +12,7 @@ process KALLISTO_INDEX { output: tuple val(meta), path("kallisto") , emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('kallisto'), eval('kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//"'), emit: versions_kallisto, topic: versions when: task.ext.when == null || task.ext.when @@ -25,20 +25,10 @@ process KALLISTO_INDEX { $args \\ -i kallisto \\ $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS """ stub: """ mkdir kallisto - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index 1e4a100902f2..99d9e773b4c7 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -6,9 +6,9 @@ keywords: - index tools: - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq - data, or more generally of target sequences using high-throughput sequencing - reads. + description: Quantifying abundances of transcripts from bulk and single-cell + RNA-Seq data, or more generally of target sequences using high-throughput + sequencing reads. homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto @@ -36,13 +36,29 @@ output: type: directory description: Kallisto genome index pattern: "*.idx" + versions_kallisto: + - - ${task.process}: + type: string + description: The name of the process + - kallisto: + type: string + description: The name of the tool + - kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - kallisto: + type: string + description: The name of the tool + - kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test index f1189587cc2d..37365690dbb0 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test +++ b/modules/nf-core/kallisto/index/tests/main.nf.test @@ -25,7 +25,7 @@ nextflow_process { assertAll( { assert process.success }, { assert path(process.out.index.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -48,7 +48,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.index, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test.snap b/modules/nf-core/kallisto/index/tests/main.nf.test.snap index 42ba6c3106f1..5af4c9136ee1 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test.snap +++ b/modules/nf-core/kallisto/index/tests/main.nf.test.snap @@ -1,51 +1,48 @@ { "sarscov2 transcriptome.fasta - stub": { "content": [ - { - "0": [ + [ + [ + { + "id": "transcriptome" + }, [ - { - "id": "transcriptome" - }, - [ - - ] + ] - ], - "1": [ - "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" - ], - "index": [ + ] + ], + { + "versions_kallisto": [ [ - { - "id": "transcriptome" - }, - [ - - ] + "KALLISTO_INDEX", + "kallisto", + "0.51.1" ] - ], - "versions": [ - "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-19T18:51:55.402665844" + "timestamp": "2026-01-28T17:53:06.991465" }, "sarscov2 transcriptome.fasta": { "content": [ - [ - "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" - ] + { + "versions_kallisto": [ + [ + "KALLISTO_INDEX", + "kallisto", + "0.51.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-19T18:51:42.328144373" + "timestamp": "2026-01-28T17:52:50.923273" } } \ No newline at end of file diff --git a/modules/nf-core/pigz/compress/main.nf b/modules/nf-core/pigz/compress/main.nf index 7ccfa6e99a7e..681ebe108ded 100644 --- a/modules/nf-core/pigz/compress/main.nf +++ b/modules/nf-core/pigz/compress/main.nf @@ -12,7 +12,7 @@ process PIGZ_COMPRESS { output: tuple val(meta), path("$archive"), emit: archive - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('pigz'), eval('pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"'), emit: versions_pigz, topic: versions when: task.ext.when == null || task.ext.when @@ -24,11 +24,6 @@ process PIGZ_COMPRESS { # Note: needs --stdout for pigz to avoid the following issue: # pigz: skipping: ${raw_file} is a symbolic link pigz --processes $task.cpus --stdout --force ${args} ${raw_file} > ${archive} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' ) - END_VERSIONS """ stub: @@ -36,10 +31,5 @@ process PIGZ_COMPRESS { archive = raw_file.toString() + ".gz" """ touch ${archive} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' ) - END_VERSIONS """ } diff --git a/modules/nf-core/pigz/compress/meta.yml b/modules/nf-core/pigz/compress/meta.yml index 573ae26f5c30..08794d8027d5 100644 --- a/modules/nf-core/pigz/compress/meta.yml +++ b/modules/nf-core/pigz/compress/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pigz_compress" description: Compresses files with pigz. keywords: @@ -36,13 +35,29 @@ output: pattern: "*.gz" ontologies: - edam: http://edamontology.org/format_3989 # GZIP format + versions_pigz: + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test b/modules/nf-core/pigz/compress/tests/main.nf.test index b3cb25e36675..621d02835bf0 100644 --- a/modules/nf-core/pigz/compress/tests/main.nf.test +++ b/modules/nf-core/pigz/compress/tests/main.nf.test @@ -22,7 +22,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.archive, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -44,9 +47,8 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.archive[0][1]).name, - process.out.versions - ).match() - } + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test.snap b/modules/nf-core/pigz/compress/tests/main.nf.test.snap index 4d8df9f1bb3f..0054a4364204 100644 --- a/modules/nf-core/pigz/compress/tests/main.nf.test.snap +++ b/modules/nf-core/pigz/compress/tests/main.nf.test.snap @@ -1,48 +1,47 @@ { "sarscov2 - genome - fasta": { "content": [ + [ + [ + { + "id": "test" + }, + "genome.fasta.gz:md5,6e9fe4042a72f2345f644f239272b7e6" + ] + ], { - "0": [ + "versions_pigz": [ [ - { - "id": "test" - }, - "genome.fasta.gz:md5,6e9fe4042a72f2345f644f239272b7e6" + "PIGZ_COMPRESS", + "pigz", + "2.8" ] - ], - "1": [ - "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad" - ], - "archive": [ - [ - { - "id": "test" - }, - "genome.fasta.gz:md5,6e9fe4042a72f2345f644f239272b7e6" - ] - ], - "versions": [ - "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2023-12-11T22:39:53.350546" + "timestamp": "2026-01-28T17:50:46.437661" }, "sarscov2 - genome - fasta - stub": { "content": [ "genome.fasta.gz", - [ - "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad" - ] + { + "versions_pigz": [ + [ + "PIGZ_COMPRESS", + "pigz", + "2.8" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-30T12:18:32.339508" + "timestamp": "2026-01-28T17:50:57.213069" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index a77ad8214495..384185f1e79b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX { tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval('samtools --version 2>&1 | head -1 | sed "s/^.*samtools //; s/Using.*//"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -27,11 +27,6 @@ process SAMTOOLS_INDEX { -@ ${task.cpus} \\ $args \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -40,10 +35,5 @@ process SAMTOOLS_INDEX { "crai" : args.contains("-c") ? "csi" : "bai" """ touch ${input}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 1bed6bca6348..52f239b482b1 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -60,13 +60,29 @@ output: description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version 2>&1 | head -1 | sed "s/^.*samtools //; s/Using.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version 2>&1 | head -1 | sed "s/^.*samtools //; s/Using.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5cd417..c96cec86098e 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -23,7 +23,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -43,7 +46,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -67,7 +73,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.csi[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } @@ -89,7 +95,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -110,7 +119,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -133,7 +145,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.csi, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3836c6bfeb70..afc8a1ff6d47 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,250 +1,156 @@ { "csi - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ], - "bai": [ - - ], - "crai": [ - - ], - "csi": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:38.25787" + "timestamp": "2026-01-28T17:52:10.030187" }, "crai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:34.496412" + "timestamp": "2026-01-28T17:51:59.125484" }, "bai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:25.934431" + "timestamp": "2026-01-28T17:51:47.277042" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", - [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:22.262088" + "timestamp": "2026-01-28T17:51:35.758735" }, "crai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:18.191664" + "timestamp": "2026-01-28T17:51:26.561965" }, "bai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ], - "bai": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:08.51539" + "timestamp": "2026-01-28T17:51:15.299035" } } \ No newline at end of file diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index e712ebe63ab5..b9c324dac5ba 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -12,7 +12,7 @@ process UNTAR { output: tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions + tuple val("${task.process}"), val('untar'), eval('tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//"'), emit: versions_untar, topic: versions when: task.ext.when == null || task.ext.when @@ -43,10 +43,6 @@ process UNTAR { ${args2} fi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ stub: @@ -75,10 +71,5 @@ process UNTAR { fi done fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index 1603e3829658..571d8078a42b 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -38,13 +38,29 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*/" + versions_untar: + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index c957517aaa6b..fde8db16a1a6 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -20,7 +20,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -38,7 +41,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -58,7 +64,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -78,7 +87,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index ceb91b7925ca..51a414dd4035 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,158 +1,118 @@ { "test_untar_onlyfiles": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:28.231047" + "timestamp": "2026-01-28T17:49:32.000491" }, "test_untar_onlyfiles - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:45.773103" + "timestamp": "2026-01-28T17:49:58.812479" }, "test_untar - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:36.777441" + "timestamp": "2026-01-28T17:49:48.119456" }, "test_untar": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:19.377674" + "timestamp": "2026-01-28T17:49:17.252494" } } \ No newline at end of file diff --git a/subworkflows/nf-core/archive_extract/main.nf b/subworkflows/nf-core/archive_extract/main.nf index eaff45420c65..f4fe9d84645e 100644 --- a/subworkflows/nf-core/archive_extract/main.nf +++ b/subworkflows/nf-core/archive_extract/main.nf @@ -33,7 +33,6 @@ workflow ARCHIVE_EXTRACT { UNZIP.out.unzipped_archive, ) - versions = versions.mix(UNTAR.out.versions) versions = versions.mix(UNZIP.out.versions) emit: diff --git a/subworkflows/nf-core/archive_extract/tests/main.nf.test.snap b/subworkflows/nf-core/archive_extract/tests/main.nf.test.snap index 25a18f5c1094..e2a69815ebe0 100644 --- a/subworkflows/nf-core/archive_extract/tests/main.nf.test.snap +++ b/subworkflows/nf-core/archive_extract/tests/main.nf.test.snap @@ -34,7 +34,6 @@ ], "2": [ - "versions.yml:md5,57932bc4916b101206586c2fd125ea64", "versions.yml:md5,c4d6e045349ff1d9155e3abc569f1643" ], "extracted": [ @@ -69,7 +68,6 @@ ], "versions": [ - "versions.yml:md5,57932bc4916b101206586c2fd125ea64", "versions.yml:md5,c4d6e045349ff1d9155e3abc569f1643" ] } @@ -78,6 +76,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:37:09.093586" + "timestamp": "2026-01-28T18:41:01.085719" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf index df6f8b5c5544..14c483a14140 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf @@ -24,7 +24,6 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE { // Index BAM file and run samtools stats, flagstat and idxstats // SAMTOOLS_INDEX ( UMICOLLAPSE.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) ch_bam_bai_dedup = UMICOLLAPSE.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap index a4aad63142ae..5375a56a5801 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap @@ -21,15 +21,14 @@ [ "versions.yml:md5,15a99b83c8965f9b29d0e9e6dbdef621", "versions.yml:md5,61bd927f2f2121e34d94692a62305955", - "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7", - "versions.yml:md5,71d8ff70a0f65311659c446278f10b1a" + "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:35:06.350407" + "timestamp": "2026-01-28T18:49:43.532881" }, "test_bam_dedup_stats_samtools_umicollapse_flagstats": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf index fc3fbb040a51..0d08b794209e 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf @@ -25,7 +25,6 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS { // Index BAM file and run samtools stats, flagstat and idxstats // SAMTOOLS_INDEX ( UMITOOLS_DEDUP.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) ch_bam_bai_dedup = UMITOOLS_DEDUP.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 3e30a5db80c1..588bd92b45a8 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -29,15 +29,14 @@ [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:35:42.524116" + "timestamp": "2026-01-28T18:44:13.69182" }, "sarscov2_bam_bai - stub": { "content": [ @@ -61,8 +60,7 @@ "10": [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ], "2": [ [ @@ -201,8 +199,7 @@ "versions": [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ] } ], @@ -210,6 +207,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T17:36:38.836410987" + "timestamp": "2026-01-28T18:44:44.189901" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf index f16cada551ee..bbf7f57aff08 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -23,7 +23,6 @@ workflow BAM_MARKDUPLICATES_PICARD { ch_markdup = PICARD_MARKDUPLICATES.out.bam.mix(PICARD_MARKDUPLICATES.out.cram) SAMTOOLS_INDEX ( ch_markdup ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) ch_reads_index = ch_markdup .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 5e24e12bc7cb..da4f7db4999c 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -9,15 +9,14 @@ [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:37:26.3247" + "timestamp": "2026-01-28T18:47:53.913903" }, "sarscov2 - bam - stub": { "content": [ @@ -88,7 +87,6 @@ "9": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ], "bai": [ @@ -157,16 +155,15 @@ "versions": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:37:50.805524" + "timestamp": "2026-01-28T18:48:29.686735" }, "homo_sapiens - cram - stub": { "content": [ @@ -231,7 +228,6 @@ "9": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ], "bai": [ @@ -294,16 +290,15 @@ "versions": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:38:18.069303" + "timestamp": "2026-01-28T18:49:07.899758" }, "sarscov2 - bam": { "content": [ @@ -315,14 +310,13 @@ [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:36:56.78063" + "timestamp": "2026-01-28T18:47:02.374124" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index e45794941894..8613b5db23e0 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -18,7 +18,6 @@ workflow BAM_SORT_STATS_SAMTOOLS { SAMTOOLS_SORT ( ch_bam, ch_fasta, '' ) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) SAMTOOLS_SORT.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 239f163c79d3..e6de74ce55aa 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -29,16 +29,15 @@ ] ], [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:04:39.140333" + "timestamp": "2026-01-28T18:41:41.566469" }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -70,16 +69,15 @@ ] ], [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:04:48.787289" + "timestamp": "2026-01-28T18:42:01.259964" }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -133,7 +131,6 @@ ] ], "6": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], @@ -186,7 +183,6 @@ ] ], "versions": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] @@ -194,9 +190,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:05:00.693649" + "timestamp": "2026-01-28T18:42:18.473258" }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -250,7 +246,6 @@ ] ], "6": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], @@ -303,7 +298,6 @@ ] ], "versions": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] @@ -311,8 +305,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:05:10.863912" + "timestamp": "2026-01-28T18:42:35.084852" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_split_by_region/main.nf b/subworkflows/nf-core/bam_split_by_region/main.nf index 50442c767d5e..affb3742f8db 100644 --- a/subworkflows/nf-core/bam_split_by_region/main.nf +++ b/subworkflows/nf-core/bam_split_by_region/main.nf @@ -52,7 +52,6 @@ workflow BAM_SPLIT_BY_REGION { // SAMTOOLS_INDEX(SAMTOOLS_VIEW.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) // // Emit channel in the same format as was taken in by joining each bam with its bai. diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap index 231fbf637caf..65843ab156b9 100644 --- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap @@ -17,14 +17,14 @@ "test_chr21:25689497-46709983.bam.bai" ], [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-25T15:33:47.930917" + "timestamp": "2026-01-28T18:53:22.940632" }, "homo_sapiens - test_paired_end_markduplicates_sorted_bam - stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ], "bam_bai": [ [ @@ -91,14 +91,14 @@ ] ], "versions": [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-25T15:31:05.89921" + "timestamp": "2026-01-28T18:53:42.637561" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf index 452bd64ed5b5..69a89b7a7d57 100644 --- a/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf @@ -56,7 +56,6 @@ workflow FASTA_INDEX_BISMARK_BWAMETH { ) ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR.out.untar) - ch_versions = ch_versions.mix(UNTAR.out.versions) } else { BISMARK_GENOMEPREPARATION ( ch_fasta @@ -85,7 +84,6 @@ workflow FASTA_INDEX_BISMARK_BWAMETH { ) ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR.out.untar) - ch_versions = ch_versions.mix(UNTAR.out.versions) } else { if (use_mem2) { BWAMETH_INDEX ( diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap index d075b0d302eb..5935fcc09171 100644 --- a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap @@ -46,14 +46,14 @@ ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:38:27.844391" + "timestamp": "2026-01-28T19:07:52.452246" }, "Params: bwameth | generate fasta index | download bwameth index": { "content": [ @@ -93,14 +93,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:39:59.918191" + "timestamp": "2026-01-28T19:09:40.968671" }, "Params: bwameth | generate fasta index | download bwameth mem2 index | collecthsmetrics": { "content": [ @@ -139,14 +139,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:41:00.949902" + "timestamp": "2026-01-28T19:11:05.277385" }, "Params: bwameth | generate fasta index | generate bwameth index": { "content": [ @@ -231,14 +231,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:40:07.954159" + "timestamp": "2026-01-28T19:09:58.229235" }, "Params: bismark_hisat | generate bismark index (hisat2)": { "content": [ @@ -291,14 +291,14 @@ ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:39:37.210692" + "timestamp": "2026-01-28T19:08:56.44674" }, "Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": { "content": [ @@ -338,14 +338,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:40:53.625281" + "timestamp": "2026-01-28T19:10:50.059696" }, "Params: bismark_hisat | download bismark index (hisat2)": { "content": [ @@ -398,14 +398,14 @@ ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:39:29.25205" + "timestamp": "2026-01-28T19:08:40.851749" }, "Params: bwameth | download fasta index | download bwameth index": { "content": [ @@ -445,14 +445,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:39:44.710477" + "timestamp": "2026-01-28T19:09:11.87557" }, "Params: bwameth | download fasta index | download bwameth mem2 index": { "content": [ @@ -491,14 +491,14 @@ ] ], [ - "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:39:52.043015" + "timestamp": "2026-01-28T19:09:27.279429" }, "Params: bwameth | generate fasta index | generate bwameth mem2 index": { "content": [ diff --git a/subworkflows/nf-core/fasta_index_dna/main.nf b/subworkflows/nf-core/fasta_index_dna/main.nf index 82ca069bfe4f..bf967835df13 100644 --- a/subworkflows/nf-core/fasta_index_dna/main.nf +++ b/subworkflows/nf-core/fasta_index_dna/main.nf @@ -32,7 +32,6 @@ workflow FASTA_INDEX_DNA { if (val_aligner == 'bowtie2') { BOWTIE2_BUILD(ch_fasta) ch_aligner_index = BOWTIE2_BUILD.out.index - ch_versions = BOWTIE2_BUILD.out.versions } else if (val_aligner == 'bwamem') { BWAMEM1_INDEX(ch_fasta) ch_aligner_index = BWAMEM1_INDEX.out.index diff --git a/subworkflows/nf-core/fasta_index_dna/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_dna/tests/main.nf.test.snap index 1762c3abbbcc..dc38ad37329c 100644 --- a/subworkflows/nf-core/fasta_index_dna/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_index_dna/tests/main.nf.test.snap @@ -105,7 +105,7 @@ ] ], "1": [ - "versions.yml:md5,3b091297ba4bafebe767e26c7f85a086" + ], "index": [ [ @@ -123,22 +123,18 @@ ] ], "versions": [ - "versions.yml:md5,3b091297ba4bafebe767e26c7f85a086" + ] }, [ - { - "FASTA_INDEX_DNA:BOWTIE2_BUILD": { - "bowtie2": "2.5.4" - } - } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-08-28T15:45:50.575444502" + "timestamp": "2026-01-28T19:06:17.775748" }, "Params: bwamem | generate bwamem1 index": { "content": [ @@ -207,7 +203,7 @@ ] ], "1": [ - "versions.yml:md5,3b091297ba4bafebe767e26c7f85a086" + ], "index": [ [ @@ -225,22 +221,18 @@ ] ], "versions": [ - "versions.yml:md5,3b091297ba4bafebe767e26c7f85a086" + ] }, [ - { - "FASTA_INDEX_DNA:BOWTIE2_BUILD": { - "bowtie2": "2.5.4" - } - } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-08-28T15:44:49.995784503" + "timestamp": "2026-01-28T19:04:22.355154" }, "Params: bwamem2 | generate bwamem2 index": { "content": [ diff --git a/subworkflows/nf-core/fasta_index_methylseq/main.nf b/subworkflows/nf-core/fasta_index_methylseq/main.nf index 81f9f1562967..7fe7c205acc0 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/main.nf +++ b/subworkflows/nf-core/fasta_index_methylseq/main.nf @@ -61,7 +61,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) - ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { if( aligner == "bismark_hisat") { @@ -99,7 +98,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR_BWAMETH.out.untar) - ch_versions = ch_versions.mix(UNTAR_BWAMETH.out.versions) } else { BWAMETH_INDEX ( ch_fasta, @@ -129,7 +127,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bwamem_index = ch_bwamem_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) - ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { log.info "BWA index not provided. Generating BWA index from FASTA file." BWA_INDEX ( diff --git a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap index 33405685d70d..6c55f8c32a28 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap @@ -88,14 +88,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:26.091313" + "timestamp": "2026-01-28T19:13:16.260364" }, "Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": { "content": [ @@ -138,14 +138,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:07.137329" + "timestamp": "2026-01-28T19:14:33.818185" }, "Params: bwameth | generate fasta index | generate bwameth mem2 index": { "content": [ @@ -246,14 +246,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:41:32.513035" + "timestamp": "2026-01-28T19:11:32.015248" }, "Params: bwameth | generate fasta index | download bwameth mem2 index | collecthsmetrics": { "content": [ @@ -295,14 +295,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:14.983559" + "timestamp": "2026-01-28T19:14:46.745643" }, "Params: bwameth | generate fasta index | download bwameth mem2 index": { "content": [ @@ -344,14 +344,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:33.433615" + "timestamp": "2026-01-28T19:13:33.728406" }, "Params: bwameth | generate fasta index | generate bwameth index": { "content": [ @@ -456,14 +456,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:03.741859" + "timestamp": "2026-01-28T19:12:27.636417" }, "Params: bismark_hisat | download bismark index (hisat2)": { "content": [ @@ -519,14 +519,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:41:55.807647" + "timestamp": "2026-01-28T19:12:13.719001" }, "Params: bwameth | download fasta index | download bwameth index": { "content": [ @@ -569,14 +569,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:10.926869" + "timestamp": "2026-01-28T19:12:43.242926" }, "Params: bwameth | download fasta index | download bwameth mem2 index": { "content": [ @@ -618,14 +618,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:18.694983" + "timestamp": "2026-01-28T19:12:56.644131" }, "Params: bwamem | generate fasta index | generate bwamem index": { "content": [ diff --git a/subworkflows/nf-core/fastq_align_bwaaln/main.nf b/subworkflows/nf-core/fastq_align_bwaaln/main.nf index b1f4c72788c0..44c8ac7a4ecd 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/main.nf +++ b/subworkflows/nf-core/fastq_align_bwaaln/main.nf @@ -90,7 +90,6 @@ workflow FASTQ_ALIGN_BWAALN { // Index all SAMTOOLS_INDEX ( ch_bam_for_index ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) // Remove superfluous internal maps to minimise clutter as much as possible ch_bam_for_emit = ch_bam_for_index.map{ meta, bam -> [meta - meta.subMap('key_read_ref'), bam] } diff --git a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap index bf3593a54169..40fcbc54138d 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap @@ -4,56 +4,56 @@ "1ca0f48b86ee8cf2417f72d6bf95939a", "test_test.bam.bai", [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T09:10:35.364068585" + "timestamp": "2026-01-28T18:50:18.016278" }, "test_fastq_align_bwaaln_paired_end": { "content": [ "ae4005223c9eb0f2b11bcd984e088f9c", "test_test.bam.bai", [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T09:10:47.297375297" + "timestamp": "2026-01-28T18:50:50.226213" }, "test_fastq_align_bwa_multiref": { "content": [ "88d78879c34214288644aec7ec3cb270", "test_reftest2.bam.bai", [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T09:11:19.229417206" + "timestamp": "2026-01-28T18:51:58.133971" }, "test_fastq_align_bwaaln_both": { "content": [ "ae4005223c9eb0f2b11bcd984e088f9c", "test_test.bam.bai", [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T09:11:00.513980745" + "timestamp": "2026-01-28T18:51:23.684778" }, "test_fastq_align_bwa_multiref -- stub": { "content": [ @@ -130,7 +130,7 @@ ], "3": [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ], "bai": [ [ @@ -204,21 +204,17 @@ ], "versions": [ - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" + ] }, [ - { - "FASTQ_ALIGN_BWAALN:SAMTOOLS_INDEX": { - "samtools": "1.22.1" - } - } + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T08:39:47.84242452" + "timestamp": "2026-01-28T18:52:35.140502" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_remove_rrna/main.nf b/subworkflows/nf-core/fastq_remove_rrna/main.nf index eca9913c3202..417bf56b42ee 100644 --- a/subworkflows/nf-core/fastq_remove_rrna/main.nf +++ b/subworkflows/nf-core/fastq_remove_rrna/main.nf @@ -150,7 +150,6 @@ workflow FASTQ_REMOVE_RRNA { ) ch_bowtie2_index = BOWTIE2_BUILD.out.index.first() ch_bowtie2_index_out = BOWTIE2_BUILD.out.index - ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions.first()) } // Branch reads by single-end vs paired-end for different filtering strategies diff --git a/subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test.snap index 95554e5a8c5e..d8e5b2a4bbe8 100644 --- a/subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test.snap @@ -4,7 +4,6 @@ [ "versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b", "versions.yml:md5,5edeace71a857688bae03f7a5c102caf", - "versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af", "versions.yml:md5,cb634680924d1a6f4c7de81a23a2e992" ], "bdea4e3bbdbb7c301ff578b9d8976fb6" @@ -13,7 +12,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-10T15:48:50.273951118" + "timestamp": "2026-01-28T19:03:59.369094" }, "homo_sapiens single-end [fastq] sortmerna": { "content": [ @@ -35,7 +34,6 @@ "versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b", "versions.yml:md5,5edeace71a857688bae03f7a5c102caf", "versions.yml:md5,5edeace71a857688bae03f7a5c102caf", - "versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af", "versions.yml:md5,a9810676328a1650fc826978ae8eb96b", "versions.yml:md5,bee00b6ec637b583decca8bd9c9eacd0" ] @@ -44,7 +42,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-10T15:49:36.940527491" + "timestamp": "2026-01-28T19:08:16.534623" }, "homo_sapiens paired-end [fastq] sortmerna": { "content": [ @@ -79,7 +77,6 @@ [ "versions.yml:md5,2cfbbdad4c4dcdfacedeb20ec188145b", "versions.yml:md5,5edeace71a857688bae03f7a5c102caf", - "versions.yml:md5,98dd18ffc97251b8a24e611b27ba12af", "versions.yml:md5,a9810676328a1650fc826978ae8eb96b", "versions.yml:md5,bee00b6ec637b583decca8bd9c9eacd0" ], @@ -90,6 +87,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-10T15:48:40.498006186" + "timestamp": "2026-01-28T19:03:20.029169" } } \ No newline at end of file From 2e0e5ec1150c7d041c214c7acb5d12ff047fe3b8 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 29 Jan 2026 09:25:23 +0000 Subject: [PATCH 2/6] Remove SAMTOOLS_INDEX version collection from additional subworkflows Remove .out.versions references from fastq_align_dedup_bismark and fastq_align_dedup_bwamem since samtools/index now uses topic-based version emission. Co-Authored-By: Claude Opus 4.5 --- subworkflows/nf-core/fastq_align_dedup_bismark/main.nf | 1 - subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf | 1 - 2 files changed, 2 deletions(-) diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf index c08686cb542f..af655118967d 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf @@ -70,7 +70,6 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) /* * Run bismark_methylation_extractor diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf index 32b1cf966bbf..0d46bec1f9c9 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf @@ -98,7 +98,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { ch_alignment = PICARD_MARKDUPLICATES.out.bam ch_alignment_index = SAMTOOLS_INDEX.out.bai ch_picard_metrics = PICARD_MARKDUPLICATES.out.metrics - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) } /* From efd026c6898e347f6cb875f0d6eeba9b71bea1a6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 29 Jan 2026 09:41:55 +0000 Subject: [PATCH 3/6] Remove SAMTOOLS_INDEX version collection from fastq_align_dedup_bwameth Remove aliased SAMTOOLS_INDEX_ALIGNMENTS and SAMTOOLS_INDEX_DEDUPLICATED .out.versions references since samtools/index now uses topic-based version emission. Co-Authored-By: Claude Opus 4.5 --- subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf index cf66c5035360..5ed1e8ee1331 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf @@ -70,7 +70,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { ch_alignment ) ch_alignment_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) /* * Run samtools flagstat @@ -109,7 +108,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { ch_alignment_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai ch_picard_metrics = PICARD_MARKDUPLICATES.out.metrics ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) } /* From b31933be811d1353312f0fb14470d7f2644b35e3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 29 Jan 2026 09:51:33 +0000 Subject: [PATCH 4/6] ci: Temporarily increase max_shards to 32 to reduce disk space issues This change doubles the number of shards from 16 to 32 to reduce disk pressure on CI runners. This should be reverted before merging. Co-Authored-By: Claude Opus 4.5 --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 2629ee965465..058b39ba4d2f 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,7 +77,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 16 + max_shards: 32 paths: "${{ join(fromJson(steps.list.outputs.components ), ' ') }}" - name: debug From 432569b991f2d4c429c313eb85c6dbfb3d41e57e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 29 Jan 2026 10:26:54 +0000 Subject: [PATCH 5/6] Update snaps --- .../bam_dedup_umi/tests/main.nf.test.snap | 11 ++-- .../tests/main.nf.test.snap | 56 ++++++++----------- .../tests/main.nf.test.snap | 21 ++----- .../tests/main.nf.test.snap | 23 +++----- 4 files changed, 43 insertions(+), 68 deletions(-) diff --git a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap index 45dd1fc595eb..225217702f56 100644 --- a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap @@ -27,7 +27,6 @@ ] ], [ - "versions.yml:md5,0807c0719cb97d193fd38e6588f15521", "versions.yml:md5,1a58acadd4b29b9fa08966dc33d30c1f", "versions.yml:md5,7eaf0c81f627dde8e2710a57e19b4d87", "versions.yml:md5,98c3ba7c6b08a4638ab37ee3fef1213c" @@ -35,9 +34,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-26T14:40:15.086389" + "timestamp": "2026-01-29T10:22:01.923338574" }, "sarscov2_bam_bai - umitools - with transcriptome bams": { "content": [ @@ -86,8 +85,6 @@ ] ], [ - "versions.yml:md5,2b80da6b65aeb7abca04a2d9f1619fbc", - "versions.yml:md5,50f79167a70eef4c0b788f9b206416ba", "versions.yml:md5,5e97f36286ca959f8dac4c43c54d020f", "versions.yml:md5,69d8142e036d91a3b4d1f41320bcf495", "versions.yml:md5,75264687081ce1cddb24c191058a9926", @@ -98,8 +95,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-26T14:39:15.42054" + "timestamp": "2026-01-29T10:21:53.788504682" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap index 3067314eeae6..c589b800115a 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap @@ -85,15 +85,14 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:54:08.096501" + "timestamp": "2026-01-29T09:58:24.268123607" }, "Params: bismark paired-end | default": { "content": [ @@ -181,15 +180,14 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:51:46.486572" + "timestamp": "2026-01-29T09:56:26.360038748" }, "Params: bismark single-end | default": { "content": [ @@ -277,15 +275,14 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-26T16:05:20.086401" + "timestamp": "2026-01-29T09:55:57.979733195" }, "Params: bismark paired-end | cytosine_report": { "content": [ @@ -386,15 +383,14 @@ "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,98d47ffab77641e343e4c977eee677a6", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,98d47ffab77641e343e4c977eee677a6" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:52:56.128659" + "timestamp": "2026-01-29T09:57:25.353846082" }, "Params: bismark_hisat paired-end | cytosine_report": { "content": [ @@ -495,15 +491,14 @@ "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,98d47ffab77641e343e4c977eee677a6", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,98d47ffab77641e343e4c977eee677a6" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:55:18.043595" + "timestamp": "2026-01-29T09:59:22.648148305" }, "Params: bismark_hisat paired-end | skip_deduplication": { "content": [ @@ -589,15 +584,14 @@ [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:54:41.001127" + "timestamp": "2026-01-29T09:58:51.977309125" }, "Params: bismark paired-end | skip_deduplication": { "content": [ @@ -683,15 +677,14 @@ [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:52:19.185514" + "timestamp": "2026-01-29T09:56:54.268496454" }, "Params: bismark_hisat single-end | default": { "content": [ @@ -779,14 +772,13 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-26T16:08:32.039526" + "timestamp": "2026-01-29T09:57:55.872413474" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap index 46fda1f8ac21..8506ed0b8d00 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap @@ -46,15 +46,14 @@ [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-03T18:07:22.444845091" + "timestamp": "2026-01-29T10:00:38.979590521" }, "Params: bwamem paired-end - skip_deduplication": { "content": [ @@ -183,7 +182,6 @@ "7": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ], "bai": [ @@ -257,7 +255,6 @@ "versions": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] }, @@ -273,11 +270,6 @@ "samtools": "1.22.1" } }, - { - "FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX": { - "samtools": "1.22.1" - } - }, { "FASTQ_ALIGN_DEDUP_BWAMEM:PICARD_ADDORREPLACEREADGROUPS": { "picard": "3.4.0" @@ -287,9 +279,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-03T18:08:01.772454395" + "timestamp": "2026-01-29T10:01:16.122586952" }, "Params: bwamem paired-end - default": { "content": [ @@ -338,14 +330,13 @@ [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-03T18:07:38.589146631" + "timestamp": "2026-01-29T10:00:54.230887114" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap index 885df4ab2064..81c8209660da 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap @@ -36,16 +36,14 @@ [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-11-01T03:09:53.217361" + "timestamp": "2026-01-29T09:43:40.437791602" }, "Params: bwameth paired-end | skip_deduplication": { "content": [ @@ -82,15 +80,14 @@ ], [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:40:33.660146" + "timestamp": "2026-01-29T09:44:01.715748974" }, "Params: bwameth paired-end | default": { "content": [ @@ -129,15 +126,13 @@ [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-03T12:40:19.798072" + "timestamp": "2026-01-29T09:43:52.823182122" } } \ No newline at end of file From 7f8b790d1962c2f98ef11d1c1dd9a13a714ec6e0 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 29 Jan 2026 10:38:17 +0000 Subject: [PATCH 6/6] style: Fix prettier formatting in bowtie2/build meta.yml Co-Authored-By: Claude Opus 4.5 --- modules/nf-core/bowtie2/build/meta.yml | 54 +++++++++++++------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 6e0401e4976c..3a9d31cf53ad 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -1,31 +1,31 @@ name: bowtie2_build description: Builds bowtie index for reference genome keywords: -- build -- index -- fasta -- genome -- reference + - build + - index + - fasta + - genome + - reference tools: -- bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ["GPL-3.0-or-later"] - identifier: "" -input: -- - meta: - type: map + - bowtie2: description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - ontologies: [] + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + ontologies: [] output: index: - - meta: @@ -62,8 +62,8 @@ topics: description: The expression to obtain the version of the tool authors: -- "@joseespinosa" -- "@drpatelh" + - "@joseespinosa" + - "@drpatelh" maintainers: -- "@joseespinosa" -- "@drpatelh" + - "@joseespinosa" + - "@drpatelh"