diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 6893b0475f8f..d3ac19fe6a87 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -14,11 +14,10 @@ process BWA_MEM { val sort_bam output: - tuple val(meta), path("*.bam") , emit: bam, optional: true - tuple val(meta), path("*.cram") , emit: cram, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - tuple val(meta), path("*.crai") , emit: crai, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.{sam,bam,cram}"), emit: output + tuple val(meta), path("*.{csi,bai,crai}"), emit: index , optional: true + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -43,13 +42,11 @@ process BWA_MEM { -t $task.cpus \\ \$INDEX \\ $reads \\ - | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + | samtools $samtools_command \\ + $args2 \\ + ${reference} \\ + --threads $task.cpus \\ + -o ${prefix}.${extension} - """ stub: @@ -60,15 +57,10 @@ process BWA_MEM { sort_bam && args2.contains("-O cram")? "cram": !sort_bam && args2.contains("-C") ? "cram": "bam" + def index_cmd = extension == "bam" ? "touch ${prefix}.csi" : + extension == "cram" ? "touch ${prefix}.crai" : "" """ touch ${prefix}.${extension} - touch ${prefix}.csi - touch ${prefix}.crai - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + ${index_cmd} """ } diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index e1265ab79f3b..9ca0addb720d 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -60,57 +60,71 @@ input: description: use samtools sort (true) or samtools view (false) pattern: "true or false" output: - bam: + output: - - meta: type: map description: Groovy Map containing sample information - - "*.bam": + - "*.{sam,bam,cram}": type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + description: Output SAM/BAM/CRAM file containing read alignments + pattern: "*.{sam,bam,cram}" ontologies: - edam: "http://edamontology.org/format_2572" # BAM - cram: - - - meta: - type: file - description: Output BAM file containing read alignments - ontologies: [] - - "*.cram": - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" - ontologies: - edam: "http://edamontology.org/format_3462" # CRAM - csi: + index: - - meta: type: map description: Groovy Map containing sample information - - "*.csi": + - "*.{csi,bai,crai}": type: file - description: Optional index file for BAM file - pattern: "*.{csi}" - ontologies: [] - crai: - - - meta: - type: map - description: Groovy Map containing sample information - - "*.crai": - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + description: Optional index file for BAM/CRAM file + pattern: "*.{csi,bai,crai}" ontologies: [] + versions_bwa: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate 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 process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + authors: - "@drpatelh" - "@jeremy1805" - "@matthdsm" maintainers: - - "@drpatelh" - "@jeremy1805" - "@matthdsm" diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index d7b69b9ebca6..6c1c222374b4 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -45,11 +45,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.cram, - process.out.csi, - process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getReadsMD5() + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") }, + bam(process.out.output[0][1]).getReadsMD5() ).match() } ) @@ -79,10 +77,8 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.cram, - process.out.csi, - process.out.crai, - process.out.versions, + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -114,11 +110,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.cram, - process.out.csi, - process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getReadsMD5() + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") }, + bam(process.out.output[0][1]).getReadsMD5() ).match() } ) @@ -149,11 +143,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.cram, - process.out.csi, - process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getReadsMD5() + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") }, + bam(process.out.output[0][1]).getReadsMD5() ).match() } ) @@ -184,11 +176,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.cram, - process.out.csi, - process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getReadsMD5() + process.out.index, + process.out.findAll { key, val -> key.startsWith("versions") }, + bam(process.out.output[0][1]).getReadsMD5() ).match() } ) diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap index 70b7b89b95a8..62219818c383 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -4,22 +4,29 @@ [ ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" - ], + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "798439cbd7fd81cbcc5078022dc5479d" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T15:16:52.718077761" + "timestamp": "2026-01-27T09:47:48.326542677" }, "Single-End Sort": { "content": [ @@ -48,44 +55,58 @@ [ ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" - ], + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T15:17:08.162122031" + "timestamp": "2026-01-27T09:48:03.074486887" }, "Paired-End Sort": { "content": [ [ ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" - ], + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "af8628d9df18b2d3d4f6fd47ef2bb872" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T15:17:15.713464923" + "timestamp": "2026-01-27T09:48:10.418562013" }, "Single-end - stub": { "content": [ @@ -100,9 +121,6 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test", @@ -111,80 +129,88 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ + "2": [ [ - { - "id": "test", - "single_end": true - }, - "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "BWA_MEM", + "bwa", + "0.7.19-r1273" ] ], - "4": [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" + "3": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], - "bam": [ + "index": [ [ { "id": "test", "single_end": true }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "crai": [ + "output": [ [ { "id": "test", "single_end": true }, - "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "cram": [ - - ], - "csi": [ + "versions_bwa": [ [ - { - "id": "test", - "single_end": true - }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "BWA_MEM", + "bwa", + "0.7.19-r1273" ] ], - "versions": [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:51.638917351" + "timestamp": "2026-01-27T09:05:08.798707198" }, "Paired-End - no fasta": { "content": [ [ ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" - ], + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T15:17:23.395002931" + "timestamp": "2026-01-27T09:48:17.617556094" }, "Paired-end - stub": { "content": [ @@ -199,9 +225,6 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test", @@ -210,57 +233,58 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ + "2": [ [ - { - "id": "test", - "single_end": false - }, - "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "BWA_MEM", + "bwa", + "0.7.19-r1273" ] ], - "4": [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" + "3": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], - "bam": [ + "index": [ [ { "id": "test", "single_end": false }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "crai": [ + "output": [ [ { "id": "test", "single_end": false }, - "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "cram": [ - - ], - "csi": [ + "versions_bwa": [ [ - { - "id": "test", - "single_end": false - }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "BWA_MEM", + "bwa", + "0.7.19-r1273" ] ], - "versions": [ - "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:59.642014144" + "timestamp": "2026-01-27T09:05:16.291355375" } } \ No newline at end of file diff --git a/modules/nf-core/umitools/group/tests/main.nf.test b/modules/nf-core/umitools/group/tests/main.nf.test index 9ba95f871ea4..7c16783d2551 100644 --- a/modules/nf-core/umitools/group/tests/main.nf.test +++ b/modules/nf-core/umitools/group/tests/main.nf.test @@ -58,7 +58,7 @@ nextflow_process { script "../../../samtools/index/main.nf" process { """ - input[0] = BWA_MEM.out.bam + input[0] = BWA_MEM.out.output """ } } @@ -99,7 +99,7 @@ nextflow_process { when { process { """ - input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]) + input[0] = BWA_MEM.out.output.join(SAMTOOLS_INDEX.out.bai, by: [0]) input[1] = true input[2] = false """ @@ -124,7 +124,7 @@ nextflow_process { when { process { """ - input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]) + input[0] = BWA_MEM.out.output.join(SAMTOOLS_INDEX.out.bai, by: [0]) input[1] = true input[2] = true """ diff --git a/subworkflows/nf-core/fastq_align_bamcmp_bwa/main.nf b/subworkflows/nf-core/fastq_align_bamcmp_bwa/main.nf index f7123fac715d..3b4cbd5225dc 100644 --- a/subworkflows/nf-core/fastq_align_bamcmp_bwa/main.nf +++ b/subworkflows/nf-core/fastq_align_bamcmp_bwa/main.nf @@ -23,14 +23,12 @@ workflow FASTQ_ALIGN_BAMCMP_BWA { // BWA_MEM_PRIMARY ( ch_reads, ch_primary_index, ch_fasta, true ) - ch_versions = ch_versions.mix(BWA_MEM_PRIMARY.out.versions) // // Map reads with BWA to the contaminant index, must be queryname sorted (controlled by config) // BWA_MEM_CONTAMINANT ( ch_reads, ch_contaminant_index, [[], [] ], true ) - ch_versions = ch_versions.mix(BWA_MEM_CONTAMINANT.out.versions) // // Use BAMCMP to retain only reads which map better to the primary genome. @@ -39,14 +37,14 @@ workflow FASTQ_ALIGN_BAMCMP_BWA { // so they would be retained if they map badly to the primary genome, but with MAPQ > 0. // - ch_both_bams = BWA_MEM_PRIMARY.out.bam.join(BWA_MEM_CONTAMINANT.out.bam, by: [0], failOnDuplicate:true, failOnMismatch:true) + ch_both_bams = BWA_MEM_PRIMARY.out.output.join(BWA_MEM_CONTAMINANT.out.output, by: [0], failOnDuplicate:true, failOnMismatch:true) BAMCMP(ch_both_bams) // // Sort, index primary unfiltered BAM file and run samtools stats, flagstat and idxstats // - BAM_SORT_STATS_SAMTOOLS_UNFILTERED ( BWA_MEM_PRIMARY.out.bam, ch_fasta ) + BAM_SORT_STATS_SAMTOOLS_UNFILTERED ( BWA_MEM_PRIMARY.out.output, ch_fasta ) ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS_UNFILTERED.out.versions) // diff --git a/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap index c12041b2a70b..a9e73c6a704e 100644 --- a/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap @@ -61,12 +61,10 @@ ] ], [ - "versions.yml:md5,1517fe0078871eb5fc84e0454d3c3dd6", "versions.yml:md5,1e009c9c98d6ef8695147d1c2512cfeb", "versions.yml:md5,651abc85c3ce748c6468458dfd26cdff", "versions.yml:md5,6957707ab955f91c07bf882ac126acb1", "versions.yml:md5,75b177b84a3847f3948c9f736f09508f", - "versions.yml:md5,d9ad9260e6695aa2488c08fdf95ce195", "versions.yml:md5,e3ae7f8c33cc78a9cfbf6b8782e29e86", "versions.yml:md5,f3f962e004e27ec01651a51796e240c3" ] @@ -75,6 +73,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T17:38:50.075233353" + "timestamp": "2026-01-27T10:37:27.316444252" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bwa/main.nf b/subworkflows/nf-core/fastq_align_bwa/main.nf index c7408d085fff..3d1c7c75e206 100644 --- a/subworkflows/nf-core/fastq_align_bwa/main.nf +++ b/subworkflows/nf-core/fastq_align_bwa/main.nf @@ -13,25 +13,23 @@ workflow FASTQ_ALIGN_BWA { ch_fasta // channel (optional) : [ val(meta3), path(fasta) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Map reads with BWA // BWA_MEM ( ch_reads, ch_index, ch_fasta, val_sort_bam ) - ch_versions = ch_versions.mix(BWA_MEM.out.versions.first()) // // Sort, index BAM file and run samtools stats, flagstat and idxstats // - BAM_SORT_STATS_SAMTOOLS ( BWA_MEM.out.bam, ch_fasta ) + BAM_SORT_STATS_SAMTOOLS ( BWA_MEM.out.output, ch_fasta ) ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) emit: - bam_orig = BWA_MEM.out.bam // channel: [ val(meta), path(bam) ] - + bam_orig = BWA_MEM.out.output // channel: [ val(meta), path(bam) ] bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), path(bam) ] bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), path(bai) ] csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), path(csi) ] diff --git a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap index 26866be142f5..308c3524bcfa 100644 --- a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" + "test.bam:md5,0f19bea682a4a8eda31dfb6568d0bb55" ] ], "1": [ @@ -17,7 +17,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" + "test.sorted.bam:md5,395c036482222bdff7ed1e5fa4d1cbd7" ] ], "2": [ @@ -26,7 +26,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" + "test.sorted.bam.bai:md5,0f4dccb4c3660b7d1cc78e1921e38ca5" ] ], "3": [ @@ -62,7 +62,6 @@ "7": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ], "bai": [ @@ -71,7 +70,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" + "test.sorted.bam.bai:md5,0f4dccb4c3660b7d1cc78e1921e38ca5" ] ], "bam": [ @@ -80,7 +79,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" + "test.sorted.bam:md5,395c036482222bdff7ed1e5fa4d1cbd7" ] ], "bam_orig": [ @@ -89,7 +88,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" + "test.bam:md5,0f19bea682a4a8eda31dfb6568d0bb55" ] ], "csi": [ @@ -125,16 +124,15 @@ "versions": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:43:05.771242" + "timestamp": "2026-01-27T09:49:41.972840291" }, "fastq_align_bwa_single_end": { "content": [ @@ -145,7 +143,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" + "test.bam:md5,b9885dffef48c2e847f040b2699d622f" ] ], "1": [ @@ -154,7 +152,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" + "test.sorted.bam:md5,24779266b70d4bb6456db5f6620999c9" ] ], "2": [ @@ -163,7 +161,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam.bai:md5,f79a40341ecfaae11d8621b138d4c2ea" + "test.sorted.bam.bai:md5,b494353fbd79e354c8c0add290687426" ] ], "3": [ @@ -199,7 +197,6 @@ "7": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ], "bai": [ @@ -208,7 +205,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam.bai:md5,f79a40341ecfaae11d8621b138d4c2ea" + "test.sorted.bam.bai:md5,b494353fbd79e354c8c0add290687426" ] ], "bam": [ @@ -217,7 +214,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" + "test.sorted.bam:md5,24779266b70d4bb6456db5f6620999c9" ] ], "bam_orig": [ @@ -226,7 +223,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" + "test.bam:md5,b9885dffef48c2e847f040b2699d622f" ] ], "csi": [ @@ -262,15 +259,14 @@ "versions": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:42:37.663363" + "timestamp": "2026-01-27T09:49:29.279297893" } } \ 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..1f99758013e2 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 @@ -45,16 +45,16 @@ ], [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", - "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", + "versions.yml:md5,d426e5786c34d6799617b90c3850a81b", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:07:22.444845091" + "timestamp": "2026-01-27T09:50:02.246112769" }, "Params: bwamem paired-end - skip_deduplication": { "content": [ @@ -100,14 +100,14 @@ "test.stats" ], [ - "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833" + "versions.yml:md5,d426e5786c34d6799617b90c3850a81b" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:07:48.375738382" + "timestamp": "2026-01-27T09:50:35.812847827" }, "Params: bwamem single-end - default - stub": { "content": [ @@ -182,8 +182,8 @@ ], "7": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", - "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", + "versions.yml:md5,d426e5786c34d6799617b90c3850a81b", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ], "bai": [ @@ -256,8 +256,8 @@ ], "versions": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", - "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", + "versions.yml:md5,d426e5786c34d6799617b90c3850a81b", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] }, @@ -268,13 +268,12 @@ } }, { - "FASTQ_ALIGN_DEDUP_BWAMEM:FASTQ_ALIGN_BWA:BWA_MEM": { - "bwa": "0.7.19-r1273", + "FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX": { "samtools": "1.22.1" } }, { - "FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX": { + "FASTQ_ALIGN_DEDUP_BWAMEM:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX": { "samtools": "1.22.1" } }, @@ -287,9 +286,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:08:01.772454395" + "timestamp": "2026-01-27T09:07:00.387804903" }, "Params: bwamem paired-end - default": { "content": [ @@ -337,15 +336,15 @@ ], [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", - "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", + "versions.yml:md5,d426e5786c34d6799617b90c3850a81b", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:07:38.589146631" + "timestamp": "2026-01-27T09:50:22.545128258" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dna/main.nf b/subworkflows/nf-core/fastq_align_dna/main.nf index 526f0bb8d942..8b74d30ae4ab 100644 --- a/subworkflows/nf-core/fastq_align_dna/main.nf +++ b/subworkflows/nf-core/fastq_align_dna/main.nf @@ -24,10 +24,10 @@ workflow FASTQ_ALIGN_DNA { main: - ch_bam_index = Channel.empty() - ch_bam = Channel.empty() - ch_reports = Channel.empty() - ch_versions = Channel.empty() + ch_bam_index = channel.empty() + ch_bam = channel.empty() + ch_reports = channel.empty() + ch_versions = channel.empty() // Align fastq files to reference genome and (optionally) sort if (aligner == 'bowtie2') { @@ -37,9 +37,8 @@ workflow FASTQ_ALIGN_DNA { } else if (aligner == 'bwamem'){ BWAMEM1_MEM (ch_reads, ch_aligner_index, ch_fasta, sort) // If aligner is bwa-mem - ch_bam = ch_bam.mix(BWAMEM1_MEM.out.bam) - ch_bam_index = ch_bam_index.mix(BWAMEM1_MEM.out.csi) - ch_versions = ch_versions.mix(BWAMEM1_MEM.out.versions) + ch_bam = ch_bam.mix(BWAMEM1_MEM.out.output) + ch_bam_index = ch_bam_index.mix(BWAMEM1_MEM.out.index) } else if (aligner == 'bwamem2'){ BWAMEM2_MEM (ch_reads, ch_aligner_index, ch_fasta, sort) // If aligner is bwa-mem2 diff --git a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap index 9e34d924e84a..e3e752d5cffc 100644 --- a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5,f07ba490699f918eb329e63d45a05216" ] ], "1": [ @@ -64,7 +64,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5,f07ba490699f918eb329e63d45a05216" ] ], "bam_index": [ @@ -79,10 +79,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T14:32:08.743821" + "timestamp": "2026-01-27T09:08:41.414512731" }, "test_fastq_align_bwa_mem_SE": { "content": [ @@ -191,7 +191,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam:md5,df969e7e799a733f01d807713cdd8569" ] ], "1": [ @@ -209,7 +209,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam:md5,df969e7e799a733f01d807713cdd8569" ] ], "bam_index": [ @@ -224,10 +224,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T12:03:34.617919741" + "timestamp": "2026-01-27T09:08:27.564394233" }, "test_fastq_align_strobealign_SE": { "content": [ @@ -238,7 +238,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam:md5,d24feb4a26a4e77df8ef4083d6fb7b6f" ] ], "1": [ @@ -256,7 +256,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam:md5,d24feb4a26a4e77df8ef4083d6fb7b6f" ] ], "bam_index": [ @@ -271,10 +271,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T14:32:01.424171" + "timestamp": "2026-01-27T09:08:34.745548561" }, "test_fastq_align_snapaligner_SE": { "content": [ @@ -285,7 +285,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5,b620983ca2b7c4bc1a60ab740b04a857" ] ], "1": [ @@ -303,7 +303,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5,b620983ca2b7c4bc1a60ab740b04a857" ] ], "bam_index": [ @@ -318,9 +318,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T12:03:25.88186957" + "timestamp": "2026-01-27T09:08:19.593965189" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf index 9eafbb6ce27b..734ba8c2ed41 100644 --- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf +++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf @@ -69,8 +69,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO { // the aligner should be set with the following parameters "-p -K 150000000 -Y" // to be configured in ext.args of your config BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, fasta, false ) - ch_versions = ch_versions.mix(BWAMEM1_MEM_PRE.out.versions) - aligned_bam = aligned_bam.mix(BWAMEM1_MEM_PRE.out.bam) + aligned_bam = aligned_bam.mix(BWAMEM1_MEM_PRE.out.output) } else { if(!bwa_index){ @@ -132,8 +131,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO { if (aligner == "bwa-mem") { // index made available through previous steps BWAMEM1_MEM_POST ( BAM2FASTQ_POST.out.fastq, bwaindex, fasta, false ) - ch_versions = ch_versions.mix(BWAMEM1_MEM_POST.out.versions) - aligned_bam_post = BWAMEM1_MEM_POST.out.bam + aligned_bam_post = BWAMEM1_MEM_POST.out.output } else { // index made available through previous steps BWAMEM2_MEM_POST ( BAM2FASTQ_POST.out.fastq, bwaindex, fasta, false ) diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/tests/main.nf.test.snap index 034a4ac4b59d..d642e340cd82 100644 --- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/tests/main.nf.test.snap @@ -7,16 +7,14 @@ "4a0b370b4113420e1647e1834753540d", [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", - "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", - "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" + "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T17:03:17.301814682" + "timestamp": "2026-01-27T09:53:18.250899136" }, "single_umi - stub": { "content": [ @@ -59,9 +57,7 @@ ], "4": [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", - "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", - "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" + "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508" ], "consensusbam": [ [ @@ -101,9 +97,7 @@ ], "versions": [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", - "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", - "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" + "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508" ] } ], @@ -111,7 +105,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T17:04:59.27214968" + "timestamp": "2026-01-27T09:09:48.757808145" }, "duplex_umi": { "content": [ @@ -121,15 +115,13 @@ "1ef7b104086ab403a43d7595feee4d45", [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", - "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", - "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" + "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T17:04:26.882874389" + "timestamp": "2026-01-27T09:54:24.917476047" } } \ No newline at end of file