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 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..3a9d31cf53ad 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -34,17 +34,33 @@ 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" 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_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/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_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_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/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()) } /* 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/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) } /* 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 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