diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 62af1e390c5e..dc8679c6f0fe 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -14,7 +14,7 @@ process BWAMEM2_INDEX { output: tuple val(meta), path("bwamem2"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"), topic: versions, emit: versions_bwamem2 when: task.ext.when == null || task.ext.when @@ -29,11 +29,6 @@ process BWAMEM2_INDEX { $args \\ -p bwamem2/${prefix} \\ $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS """ stub: @@ -46,10 +41,5 @@ process BWAMEM2_INDEX { touch bwamem2/${prefix}.pac touch bwamem2/${prefix}.amb touch bwamem2/${prefix}.bwt.2bit.64 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index b2aa45fb6583..909169e23f15 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -39,13 +39,27 @@ output: pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" ontologies: - edam: "http://edamontology.org/data_3210" # Genome index - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_bwamem2: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa-mem2: + type: string + description: The tool name + - bwa-mem2 version 2>&1 | tail -1: + type: string + description: The command used to generate the version of the tool +topics: + - versions: + - - process: + type: string + description: The process the versions were collected from + - tool: + type: string + description: The tool name + - version: + type: string + description: The version of the tool authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test index adf447851de1..3ee91048a72c 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test @@ -24,11 +24,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.index, - process.out.versions, - path(process.out.versions[0]).yaml - ).match() } + { assert snapshot(process.out).match() } ) } } @@ -51,11 +47,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.index, - process.out.versions, - path(process.out.versions[0]).yaml - ).match() } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap index 9ad8b20c0ed7..53eb90027ae3 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap @@ -1,64 +1,108 @@ { "fasta - stub": { "content": [ - [ - [ - { - "id": "test" - }, + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWAMEM2_INDEX", + "bwa-mem2", + "2.2.1" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions1": [ [ - "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + "BWAMEM2_INDEX", + "bwa-mem2", + "2.2.1" ] ] - ], - [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" - ], - { - "BWAMEM2_INDEX": { - "bwamem2": "2.2.1" - } } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T08:55:53.219699135" + "timestamp": "2025-09-30T15:48:12.646279004" }, "fasta": { "content": [ - [ - [ - { - "id": "test" - }, + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8", + "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216", + "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66" + ] + ] + ], + "1": [ + [ + "BWAMEM2_INDEX", + "bwa-mem2", + "2.2.1" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8", + "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216", + "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66" + ] + ] + ], + "versions1": [ [ - "genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8", - "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", - "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567", - "genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216", - "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66" + "BWAMEM2_INDEX", + "bwa-mem2", + "2.2.1" ] ] - ], - [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" - ], - { - "BWAMEM2_INDEX": { - "bwamem2": "2.2.1" - } } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-04T08:55:45.007921901" + "timestamp": "2025-09-30T15:48:02.557291528" } } \ No newline at end of file diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 27910cf6cd61..2150337db60b 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -19,7 +19,8 @@ process BWAMEM2_MEM { tuple val(meta), path("*.cram") , emit: cram, optional:true tuple val(meta), path("*.crai") , emit: crai, optional:true tuple val(meta), path("*.csi") , emit: csi , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"), topic: versions, emit: versions_bwamem2 + tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -1 | sed 's/^.*samtools //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -46,12 +47,6 @@ process BWAMEM2_MEM { \$INDEX \\ $reads \\ | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -73,11 +68,5 @@ process BWAMEM2_MEM { """ touch ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index 6c7d17284617..52461d6092d3 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: bwamem2_mem description: Performs fastq alignment to a fasta reference using BWA keywords: @@ -118,13 +119,37 @@ output: description: Index file for BAM file pattern: "*.{csi}" ontologies: [] - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_bwamem2: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa-mem2: + type: string + description: The tool name + - bwa-mem2 version 2>&1 | tail -1: + 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 2>&1 | head -1 | sed 's/^.*samtools //': + type: string + description: The command used to generate the version of the tool +topics: + - versions: + - - process: + type: string + description: The process the versions were collected from + - tool: + type: string + description: The tool name + - version: + type: string + description: The version of the tool authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 9e0ab14aec59..ad2905aca14f 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -46,7 +46,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -75,7 +75,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -107,7 +107,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -139,7 +139,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index b7d40a6830b4..faef5453c0f5 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -3,15 +3,28 @@ "content": [ "e414c2d48e2e44c2c52c20ecd88e8bd8", "57aeef88ed701a8ebc8e2f0a381b2a6", - [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" - ] + { + "versions1": [ + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "versions2": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-23T11:44:52.73673293" + "timestamp": "2025-09-30T15:49:05.152759805" }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ @@ -44,7 +57,18 @@ ] ], "5": [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "6": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -73,57 +97,107 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" + "versions1": [ + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "versions2": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-23T11:45:14.834888709" + "timestamp": "2025-09-30T15:49:34.618029626" }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ "716ed1ef39deaad346ca7cf86e08f959", "af8628d9df18b2d3d4f6fd47ef2bb872", - [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" - ] + { + "versions1": [ + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "versions2": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-23T11:45:04.750057645" + "timestamp": "2025-09-30T15:49:20.482923698" }, "sarscov2 - fastq, index, fasta, false": { "content": [ "283a83f604f3f5338acedfee349dccf4", "798439cbd7fd81cbcc5078022dc5479d", - [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" - ] + { + "versions1": [ + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "versions2": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-23T11:44:28.57550711" + "timestamp": "2025-09-30T15:48:29.586097907" }, "sarscov2 - fastq, index, fasta, true": { "content": [ "ed99048bb552cac58e39923b550b6d5b", "94fcf617f5b994584c4e8d4044e16b4f", - [ - "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" - ] + { + "versions1": [ + [ + "BWAMEM2_MEM", + "bwa-mem2", + "2.2.1" + ] + ], + "versions2": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.04.6" }, - "timestamp": "2025-09-23T11:44:40.437183765" + "timestamp": "2025-09-30T15:48:47.724769582" } } \ No newline at end of file diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf index 0d40e8654c2e..96336e1f4409 100644 --- a/modules/nf-core/limma/differential/main.nf +++ b/modules/nf-core/limma/differential/main.nf @@ -12,13 +12,14 @@ process LIMMA_DIFFERENTIAL { tuple val(meta2), path(samplesheet), path(intensities) output: - tuple val(meta), path("*.limma.results.tsv") , emit: results - tuple val(meta), path("*.limma.mean_difference.png") , emit: md_plot - tuple val(meta), path("*.MArrayLM.limma.rds") , emit: rdata - tuple val(meta), path("*.limma.model.txt") , emit: model - tuple val(meta), path("*.R_sessionInfo.log") , emit: session_info - tuple val(meta), path("*.normalised_counts.tsv") , emit: normalised_counts, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.limma.results.tsv") , emit: results + tuple val(meta), path("*.limma.mean_difference.png") , emit: md_plot + tuple val(meta), path("*.MArrayLM.limma.rds") , emit: rdata + tuple val(meta), path("*.limma.model.txt") , emit: model + tuple val(meta), path("*.R_sessionInfo.log") , emit: session_info + tuple val(meta), path("*.normalised_counts.tsv") , emit: normalised_counts, optional: true + tuple val("${task.process}"), val('r-base'), env("R_BASE_VERSION") , topic: versions, emit: versions1 + tuple val("${task.process}"), val('bioconductor-limma'), env("BIOCONDUCTOR_LIMMA_VERSION") , topic: versions, emit: versions2 when: task.ext.when == null || task.ext.when @@ -43,16 +44,11 @@ process LIMMA_DIFFERENTIAL { close(a) a <- file("${prefix}.R_sessionInfo.log", "w") close(a) - ## VERSIONS FILE + r.version <- strsplit(version[['version.string']], ' ')[[1]][3] limma.version <- as.character(packageVersion('limma')) - writeLines( - c( - '"${task.process}":', - paste(' r-base:', r.version), - paste(' bioconductor-limma:', limma.version) - ), - 'versions.yml' - ) + + Sys.setenv('R_BASE_VERSION' = r.version) + Sys.setenv('BIOCONDUCTOR_LIMMA_VERSION' = limma.version) """ } diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de.R index d55436dcc1b8..ae93eaf866b4 100644 --- a/modules/nf-core/limma/differential/templates/limma_de.R +++ b/modules/nf-core/limma/differential/templates/limma_de.R @@ -566,13 +566,8 @@ sink() r.version <- strsplit(version[['version.string']], ' ')[[1]][3] limma.version <- as.character(packageVersion('limma')) -writeLines( - c( - '"${task.process}":', - paste(' r-base:', r.version), - paste(' bioconductor-limma:', limma.version) - ), -'versions.yml') +Sys.setenv('R_BASE_VERSION' = r.version) +Sys.setenv('BIOCONDUCTOR_LIMMA_VERSION' = limma.version) ################################################ ################################################ diff --git a/modules/nf-core/limma/differential/tests/main.nf.test b/modules/nf-core/limma/differential/tests/main.nf.test index ce58185c32de..e51e5fded0dc 100644 --- a/modules/nf-core/limma/differential/tests/main.nf.test +++ b/modules/nf-core/limma/differential/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() } + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() } ) } } @@ -97,7 +97,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") }, { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.2775254") }, { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.071547786") } @@ -159,7 +159,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") }, { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.27752") }, { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.0715477") } @@ -221,7 +221,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") }, { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.4778282") }, { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.08958278") } @@ -284,7 +284,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") }, { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.2775254") }, { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.071547786") } @@ -312,7 +312,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224241") }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.77922") }, { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") }, @@ -341,7 +341,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.84055986312942") }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7055") }, { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") }, @@ -370,7 +370,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.model, process.out.versions).match() }, + { assert snapshot(process.out.model, process.out.findAll { key, val -> key.startsWith("versions")}).match() }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.8363444336503") }, { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7360") }, { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") }, @@ -398,7 +398,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot([process.out.results, process.out.model, process.out.normalised_counts, process.out.versions]).match() } + { assert snapshot([process.out.results, process.out.model, process.out.normalised_counts, process.out.findAll { key, val -> key.startsWith("versions") }]).match() } ) } } diff --git a/modules/nf-core/limma/differential/tests/main.nf.test.snap b/modules/nf-core/limma/differential/tests/main.nf.test.snap index c9586508c163..1dc1e6ec3baf 100644 --- a/modules/nf-core/limma/differential/tests/main.nf.test.snap +++ b/modules/nf-core/limma/differential/tests/main.nf.test.snap @@ -2,24 +2,22 @@ "RNAseq - Feature Counts - formula + comparison contrast string - interaction": { "content": [ [ - [ - { - "id": "genotype_WT_KO_treatment_Control_Treated", - "formula": "~ genotype * treatment", - "comparison": "genotypeWT.treatmentTreated" - }, - "genotype_WT_KO_treatment_Control_Treated.limma.model.txt:md5,82165b8b24da8f8cffafa457290feeb3" - ] + ], - [ - "versions.yml:md5,88a6e42d753077edab8daf829cd4d943" - ] + { + "versions1": [ + + ], + "versions2": [ + + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-20T12:41:52.606512166" + "timestamp": "2025-09-30T17:14:41.889290721" }, "test_limma_differential - voom_blocking": { "content": [ @@ -231,24 +229,21 @@ "test_limma_differential": { "content": [ [ - [ - { - "id": "diagnosis_normal_uremia", - "variable": "diagnosis", - "reference": "normal", - "target": "uremia" - }, - "diagnosis_normal_uremia.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" - ] + ], - [ - "versions.yml:md5,88a6e42d753077edab8daf829cd4d943" - ] + { + "versions1": [ + + ], + "versions2": [ + + ] + } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-31T12:33:25.759977" + "timestamp": "2025-09-30T17:17:20.873003578" } } \ No newline at end of file