From 56b9245ad4e013295a0d4671baf4b43b373301ed Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Fri, 23 Jan 2026 14:23:13 +0000 Subject: [PATCH 1/6] Update bwa/index --- .../nf-core/bamcmp/tests/main.nf.test.snap | 14 ++-- .../nf-core/bwa/aln/tests/main.nf.test.snap | 24 +++---- modules/nf-core/bwa/index/main.nf | 15 +--- modules/nf-core/bwa/index/meta.yml | 27 +++++-- modules/nf-core/bwa/index/tests/main.nf.test | 28 +++++++- .../nf-core/bwa/index/tests/main.nf.test.snap | 71 ++++++++++--------- .../nf-core/bwa/mem/tests/main.nf.test.snap | 40 +++++------ .../realignsamfile/tests/main.nf.test.snap | 10 +-- subworkflows/nf-core/fasta_index_dna/main.nf | 1 - .../nf-core/fasta_index_methylseq/main.nf | 1 - .../fastq_create_umi_consensus_fgbio/main.nf | 1 - 11 files changed, 128 insertions(+), 104 deletions(-) diff --git a/modules/nf-core/bamcmp/tests/main.nf.test.snap b/modules/nf-core/bamcmp/tests/main.nf.test.snap index f5291a8a3098..69a85e7fe98b 100644 --- a/modules/nf-core/bamcmp/tests/main.nf.test.snap +++ b/modules/nf-core/bamcmp/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test_primary.bam:md5,33c554725393cbb2067df8629f36ee9a" + "test_primary.bam:md5,ec8f1988c81213a511bc51dbf9b845e9" ] ], "1": [ @@ -15,7 +15,7 @@ { "id": "test" }, - "test_contaminant.bam:md5,7ee05398c1087ede9f7a55e68f0e9cfb" + "test_contaminant.bam:md5,fa555e3ef0fe38f0793357bd02e9e06b" ] ], "2": [ @@ -26,7 +26,7 @@ { "id": "test" }, - "test_contaminant.bam:md5,7ee05398c1087ede9f7a55e68f0e9cfb" + "test_contaminant.bam:md5,fa555e3ef0fe38f0793357bd02e9e06b" ] ], "primary_filtered_bam": [ @@ -34,7 +34,7 @@ { "id": "test" }, - "test_primary.bam:md5,33c554725393cbb2067df8629f36ee9a" + "test_primary.bam:md5,ec8f1988c81213a511bc51dbf9b845e9" ] ], "versions": [ @@ -43,10 +43,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:04:20.138961947" + "timestamp": "2026-01-23T13:51:32.458695956" }, "bamcmp - stub": { "content": [ diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test.snap b/modules/nf-core/bwa/aln/tests/main.nf.test.snap index 01667137acb6..19d57a682d1f 100644 --- a/modules/nf-core/bwa/aln/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/aln/tests/main.nf.test.snap @@ -54,7 +54,7 @@ "id": "test", "single_end": true }, - "test.sai:md5,aaaf39b6814c96ca1a5eacc662adf926" + "test.sai:md5,f22f2e6b58252f7e36aef7589db2d1d6" ] ], "1": [ @@ -66,7 +66,7 @@ "id": "test", "single_end": true }, - "test.sai:md5,aaaf39b6814c96ca1a5eacc662adf926" + "test.sai:md5,f22f2e6b58252f7e36aef7589db2d1d6" ] ], "versions": [ @@ -75,10 +75,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T10:58:58.682259414" + "timestamp": "2026-01-23T13:51:48.790575585" }, "Paired-End": { "content": [ @@ -90,8 +90,8 @@ "single_end": false }, [ - "test.1.sai:md5,aaaf39b6814c96ca1a5eacc662adf926", - "test.2.sai:md5,b4f185d9b4cb256dd5c377070a536124" + "test.1.sai:md5,f22f2e6b58252f7e36aef7589db2d1d6", + "test.2.sai:md5,99742f271215dcb09160951b0982588f" ] ] ], @@ -105,8 +105,8 @@ "single_end": false }, [ - "test.1.sai:md5,aaaf39b6814c96ca1a5eacc662adf926", - "test.2.sai:md5,b4f185d9b4cb256dd5c377070a536124" + "test.1.sai:md5,f22f2e6b58252f7e36aef7589db2d1d6", + "test.2.sai:md5,99742f271215dcb09160951b0982588f" ] ] ], @@ -116,10 +116,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T10:59:06.545247731" + "timestamp": "2026-01-23T13:51:57.02298319" }, "Single-End -- stub": { "content": [ diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 1860ecfa4c68..6be2c43b773c 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -13,8 +13,8 @@ process BWA_INDEX { tuple val(meta), path(fasta) output: - tuple val(meta), path("bwa") , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("bwa"), emit: index + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa when: task.ext.when == null || task.ext.when @@ -29,27 +29,16 @@ process BWA_INDEX { $args \\ -p bwa/${prefix} \\ $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${fasta.baseName}" """ mkdir bwa - touch bwa/${prefix}.amb touch bwa/${prefix}.ann touch bwa/${prefix}.bwt touch bwa/${prefix}.pac touch bwa/${prefix}.sa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 1781586fa19b..f5bf7f52a9d8 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -42,17 +42,30 @@ output: pattern: "*.{amb,ann,bwt,pac,sa}" ontologies: - edam: "http://edamontology.org/data_3210" # Genome index + 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 +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 authors: - "@drpatelh" - "@maxulysse" maintainers: - - "@drpatelh" - "@maxulysse" - "@gallvp" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index af33e73ca122..e283c106d2c6 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -22,9 +22,33 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.index).match() } + ) + } + + } + + test("BWA index - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out.index).match() } ) } diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap index 8fdb482ab9c3..a0fd3c08bf3b 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -1,47 +1,48 @@ { - "BWA index": { + "BWA index - stub": { "content": [ - { - "0": [ + [ + [ + { + "id": "test" + }, [ - { - "id": "test" - }, - [ - "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", - "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", - "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", - "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", - "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" - ] + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,9a94c646009e4e01912bde135de16400" - ], - "index": [ + ] + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-23T13:52:24.610786486" + }, + "BWA index": { + "content": [ + [ + [ + { + "id": "test" + }, [ - { - "id": "test" - }, - [ - "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", - "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", - "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", - "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", - "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" - ] + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" ] - ], - "versions": [ - "versions.yml:md5,9a94c646009e4e01912bde135de16400" ] - } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:03.657185748" + "timestamp": "2026-01-23T13:52:17.683651169" } } \ No newline at end of file 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 51496a3ca02c..b2e8ad2180a3 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -13,14 +13,14 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "37b4ee1649480bd1ff98666447f64fa5", + "baf32292ad0696144b4a48e158018d9a", "798439cbd7fd81cbcc5078022dc5479d" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:11.396076472" + "timestamp": "2026-01-23T13:52:32.855953918" }, "Single-End Sort": { "content": [ @@ -36,14 +36,14 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "57106634fcaf3bf503d5487a7717c5d3", + "2476a7e0f90e9dd7882af5baa9644ffb", "94fcf617f5b994584c4e8d4044e16b4f" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:19.529514701" + "timestamp": "2026-01-23T13:52:41.147809558" }, "Paired-End": { "content": [ @@ -59,14 +59,14 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "57770ff7c7186ed40c42f3d71c16ce3c", + "a5cfed1c80d98c8f1d11b33a9ea2d0fb", "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:27.433790935" + "timestamp": "2026-01-23T13:52:49.568792316" }, "Paired-End Sort": { "content": [ @@ -82,14 +82,14 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "8f5d8f83b485dcfa1f47a73ae645e3a7", + "e606deaa1c182062bc04af00229b247b", "af8628d9df18b2d3d4f6fd47ef2bb872" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:35.775774487" + "timestamp": "2026-01-23T13:52:58.182044737" }, "Single-end - stub": { "content": [ @@ -182,14 +182,14 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "57770ff7c7186ed40c42f3d71c16ce3c", + "a5cfed1c80d98c8f1d11b33a9ea2d0fb", "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:05:43.764589371" + "timestamp": "2026-01-23T13:53:06.438732762" }, "Paired-end - stub": { "content": [ diff --git a/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test.snap b/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test.snap index fdddb24e4039..8a22206af34b 100644 --- a/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test.snap +++ b/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test.snap @@ -41,7 +41,7 @@ "id": "test", "single_end": true }, - "test_realigned.bam:md5,35ab6f68f44c91677374315930ee9e80" + "test_realigned.bam:md5,d3e3f56c34a9c24df738920caeef619c" ] ], "1": [ @@ -53,7 +53,7 @@ "id": "test", "single_end": true }, - "test_realigned.bam:md5,35ab6f68f44c91677374315930ee9e80" + "test_realigned.bam:md5,d3e3f56c34a9c24df738920caeef619c" ] ], "versions": [ @@ -62,9 +62,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:01:26.531792671" + "timestamp": "2026-01-23T13:57:04.872898095" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_index_dna/main.nf b/subworkflows/nf-core/fasta_index_dna/main.nf index 3274f8aa7a85..f70be194567a 100644 --- a/subworkflows/nf-core/fasta_index_dna/main.nf +++ b/subworkflows/nf-core/fasta_index_dna/main.nf @@ -37,7 +37,6 @@ workflow FASTA_INDEX_DNA { .map{meta, index, alt -> [meta, index + alt]} ) - ch_versions = ch_versions.mix(BWAMEM1_INDEX.out.versions) break case 'bwamem2': BWAMEM2_INDEX(ch_fasta) // If aligner is bwa-mem2 diff --git a/subworkflows/nf-core/fasta_index_methylseq/main.nf b/subworkflows/nf-core/fasta_index_methylseq/main.nf index 230cd7856e7a..81f9f1562967 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/main.nf +++ b/subworkflows/nf-core/fasta_index_methylseq/main.nf @@ -136,7 +136,6 @@ workflow FASTA_INDEX_METHYLSEQ { ch_fasta ) ch_bwamem_index = BWA_INDEX.out.index - ch_versions = ch_versions.mix(BWA_INDEX.out.versions) } } 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 50c1851a91d8..9eafbb6ce27b 100644 --- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf +++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf @@ -61,7 +61,6 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO { if(!bwa_index){ BWAMEM1_INDEX ( fasta ) - ch_versions = ch_versions.mix(BWAMEM1_INDEX.out.versions) } // sets bwaindex to correct input From ed31cf9ae7f4bcd0f39d031240f86afb34fa4d4a Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Fri, 23 Jan 2026 17:06:21 +0000 Subject: [PATCH 2/6] Swap bwa index to topic --- modules/nf-core/bwa/index/tests/main.nf.test | 4 +- .../nf-core/bwa/index/tests/main.nf.test.snap | 112 ++++++++++++++---- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test.snap | 16 +-- 4 files changed, 98 insertions(+), 42 deletions(-) diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index e283c106d2c6..f0fba82a1a59 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out.index).match() } + { assert snapshot(process.out).match() } ) } @@ -48,7 +48,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out.index).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap index a0fd3c08bf3b..21a6f73c3205 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -1,48 +1,108 @@ { "BWA index - stub": { "content": [ - [ - [ - { - "id": "test" - }, - [ - "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" ] ] - ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:24.610786486" + "timestamp": "2026-01-23T16:58:59.966558606" }, "BWA index": { "content": [ - [ - [ - { - "id": "test" - }, - [ - "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", - "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", - "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", - "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", - "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "1": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" ] ] - ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:17.683651169" + "timestamp": "2026-01-23T16:58:53.330725134" } } \ No newline at end of file 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 18bb52b04acd..33405685d70d 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 @@ -38,14 +38,14 @@ ] ], [ - "versions.yml:md5,b8e44242903aff8009b1334412f1b642" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:39.975917" + "timestamp": "2026-01-23T17:02:02.544202326" }, "Params: bwameth | generate fasta index | download bwameth index": { "content": [ @@ -666,14 +666,14 @@ ] ], [ - "versions.yml:md5,b8e44242903aff8009b1334412f1b642" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:31.376524" + "timestamp": "2026-01-23T17:01:53.325149887" }, "Params: bismark | generate bismark index (bowtie2)": { "content": [ 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 71cab66f684a..1e6a9514932d 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 @@ -7,7 +7,6 @@ "4a0b370b4113420e1647e1834753540d", [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,8cb43214ca75a610576c12e221ef0a80", "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" @@ -17,7 +16,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-14T08:19:08.337223502" + "timestamp": "2026-01-23T17:03:17.301814682" }, "single_umi - stub": { "content": [ @@ -60,7 +59,6 @@ ], "4": [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,8cb43214ca75a610576c12e221ef0a80", "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" @@ -103,7 +101,6 @@ ], "versions": [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,8cb43214ca75a610576c12e221ef0a80", "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" @@ -114,17 +111,16 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-08T21:08:35.83327882" + "timestamp": "2026-01-23T17:04:59.27214968" }, "duplex_umi": { "content": [ "74336a9d044b676abb31a44423187068", - "5f936d54c24b3bba71faca45988b6d2a", - "fde89525ff1ea23a7dcefb152263a81d", - "1ef7b104086ab403a43d7595feee4d45", + "980e5a63687e0192f749489bfff3c354", + "f24b41a7d9078175b645e3b59fd098f3", + "40e974848715319e7f3334ee084f81cd", [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", - "versions.yml:md5,8cb43214ca75a610576c12e221ef0a80", "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", "versions.yml:md5,d4002928b733d6e0449fa2c1257f1c51", "versions.yml:md5,dabd25445072e5f00a20caa8aebeb1e7" @@ -134,6 +130,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-14T08:20:17.40212184" + "timestamp": "2026-01-23T17:04:26.882874389" } } \ No newline at end of file From 27b4e241255ee2a2d8e9225c7fe543638d43a9fb Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:20:17 +0000 Subject: [PATCH 3/6] Remove header test from bwa/mem --- modules/nf-core/bwa/mem/tests/main.nf.test | 5 --- .../nf-core/bwa/mem/tests/main.nf.test.snap | 15 +++------ subworkflows/nf-core/fasta_index_dna/main.nf | 2 +- .../fasta_index_dna/tests/main.nf.test.snap | 32 +++++++------------ 4 files changed, 18 insertions(+), 36 deletions(-) diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index 5de2c2f45393..d7b69b9ebca6 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -49,7 +49,6 @@ nextflow_process { process.out.csi, process.out.crai, process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -84,7 +83,6 @@ nextflow_process { process.out.csi, process.out.crai, process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -120,7 +118,6 @@ nextflow_process { process.out.csi, process.out.crai, process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -156,7 +153,6 @@ nextflow_process { process.out.csi, process.out.crai, process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -192,7 +188,6 @@ nextflow_process { process.out.csi, process.out.crai, process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[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 b2e8ad2180a3..70b7b89b95a8 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -13,14 +13,13 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "baf32292ad0696144b4a48e158018d9a", "798439cbd7fd81cbcc5078022dc5479d" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:32.855953918" + "timestamp": "2026-01-26T15:16:52.718077761" }, "Single-End Sort": { "content": [ @@ -36,14 +35,13 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "2476a7e0f90e9dd7882af5baa9644ffb", "94fcf617f5b994584c4e8d4044e16b4f" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:41.147809558" + "timestamp": "2026-01-26T15:17:00.554958251" }, "Paired-End": { "content": [ @@ -59,14 +57,13 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "a5cfed1c80d98c8f1d11b33a9ea2d0fb", "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:49.568792316" + "timestamp": "2026-01-26T15:17:08.162122031" }, "Paired-End Sort": { "content": [ @@ -82,14 +79,13 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "e606deaa1c182062bc04af00229b247b", "af8628d9df18b2d3d4f6fd47ef2bb872" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:52:58.182044737" + "timestamp": "2026-01-26T15:17:15.713464923" }, "Single-end - stub": { "content": [ @@ -182,14 +178,13 @@ [ "versions.yml:md5,f882069f942ae2a95e2c91f82e4445c6" ], - "a5cfed1c80d98c8f1d11b33a9ea2d0fb", "57aeef88ed701a8ebc8e2f0a381b2a6" ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T13:53:06.438732762" + "timestamp": "2026-01-26T15:17:23.395002931" }, "Paired-end - stub": { "content": [ diff --git a/subworkflows/nf-core/fasta_index_dna/main.nf b/subworkflows/nf-core/fasta_index_dna/main.nf index 59374e714f93..82ca069bfe4f 100644 --- a/subworkflows/nf-core/fasta_index_dna/main.nf +++ b/subworkflows/nf-core/fasta_index_dna/main.nf @@ -36,7 +36,7 @@ workflow FASTA_INDEX_DNA { } else if (val_aligner == 'bwamem') { BWAMEM1_INDEX(ch_fasta) ch_aligner_index = BWAMEM1_INDEX.out.index - ch_versions = BWAMEM1_INDEX.out.versions + // bwa/index uses a topic channel for versions } else if (val_aligner == 'bwamem2') { BWAMEM2_INDEX(ch_fasta) ch_aligner_index = BWAMEM2_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 56cffc930441..1762c3abbbcc 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 @@ -158,7 +158,7 @@ ] ], "1": [ - "versions.yml:md5,c42ec14c72fcccaca2b8e0813fc4e9e2" + ], "index": [ [ @@ -175,22 +175,18 @@ ] ], "versions": [ - "versions.yml:md5,c42ec14c72fcccaca2b8e0813fc4e9e2" + ] }, [ - { - "FASTA_INDEX_DNA:BWAMEM1_INDEX": { - "bwa": "0.7.19-r1273" - } - } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-10-24T11:22:25.36079182" + "timestamp": "2026-01-26T15:02:43.826434447" }, "Params: bowtie2 | generate bowtie2 index": { "content": [ @@ -316,7 +312,7 @@ ] ], "1": [ - "versions.yml:md5,c42ec14c72fcccaca2b8e0813fc4e9e2" + ], "index": [ [ @@ -333,22 +329,18 @@ ] ], "versions": [ - "versions.yml:md5,c42ec14c72fcccaca2b8e0813fc4e9e2" + ] }, [ - { - "FASTA_INDEX_DNA:BWAMEM1_INDEX": { - "bwa": "0.7.19-r1273" - } - } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-10-24T11:23:04.773271413" + "timestamp": "2026-01-26T15:03:23.691963445" }, "Params: dragmap | generate dragmap hashtable - stub": { "content": [ From b5b01cc33cd26e7694ebe02798495071c7d50ab3 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 27 Jan 2026 08:50:26 +0000 Subject: [PATCH 4/6] Update fgbio snapshot --- .../tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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 1e6a9514932d..034a4ac4b59d 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 @@ -116,9 +116,9 @@ "duplex_umi": { "content": [ "74336a9d044b676abb31a44423187068", - "980e5a63687e0192f749489bfff3c354", - "f24b41a7d9078175b645e3b59fd098f3", - "40e974848715319e7f3334ee084f81cd", + "5f936d54c24b3bba71faca45988b6d2a", + "fde89525ff1ea23a7dcefb152263a81d", + "1ef7b104086ab403a43d7595feee4d45", [ "versions.yml:md5,10efd5211f01301e183fea53b6e92d03", "versions.yml:md5,c1ad3e88dc4dc0d05138b20806c6d508", From cb0bd0337f24c2c82e86d35ef4c5b53e5c9a5a39 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 27 Jan 2026 10:54:06 +0000 Subject: [PATCH 5/6] Swap bwa/mem to versions --- modules/nf-core/bwa/mem/main.nf | 32 +-- modules/nf-core/bwa/mem/meta.yml | 82 ++++--- modules/nf-core/bwa/mem/tests/main.nf.test | 38 ++- .../nf-core/bwa/mem/tests/main.nf.test.snap | 220 ++++++++++-------- .../nf-core/umitools/group/tests/main.nf.test | 6 +- .../nf-core/fastq_align_bamcmp_bwa/main.nf | 6 +- .../tests/main.nf.test.snap | 4 +- subworkflows/nf-core/fastq_align_bwa/main.nf | 8 +- .../fastq_align_bwa/tests/main.nf.test.snap | 36 ++- .../tests/main.nf.test.snap | 31 ++- subworkflows/nf-core/fastq_align_dna/main.nf | 13 +- .../fastq_align_dna/tests/main.nf.test.snap | 40 ++-- .../fastq_create_umi_consensus_fgbio/main.nf | 6 +- .../tests/main.nf.test.snap | 22 +- 14 files changed, 271 insertions(+), 273 deletions(-) diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 6893b0475f8f..a891315009fb 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 From 3d313fd65842528c012933c5ba9ca00d5a874215 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 27 Jan 2026 11:05:53 +0000 Subject: [PATCH 6/6] [automated] Fix linting with Prettier --- modules/nf-core/bwa/mem/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index a891315009fb..d3ac19fe6a87 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -57,7 +57,7 @@ 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" : + def index_cmd = extension == "bam" ? "touch ${prefix}.csi" : extension == "cram" ? "touch ${prefix}.crai" : "" """ touch ${prefix}.${extension}