From 2e19607b244838beabc4b04f54193504c9941473 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:00:20 +0200 Subject: [PATCH] Update to topics --- modules/nf-core/mageck/count/main.nf | 28 ++-- modules/nf-core/mageck/count/meta.yml | 39 +++-- .../nf-core/mageck/count/tests/main.nf.test | 23 +-- .../mageck/count/tests/main.nf.test.snap | 82 ++++------ modules/nf-core/mageck/mle/main.nf | 22 +-- modules/nf-core/mageck/mle/meta.yml | 31 +++- modules/nf-core/mageck/mle/tests/main.nf.test | 22 ++- .../mageck/mle/tests/main.nf.test.snap | 69 +++++---- modules/nf-core/mageck/test/main.nf | 12 +- modules/nf-core/mageck/test/meta.yml | 35 +++-- .../nf-core/mageck/test/tests/main.nf.test | 54 +++---- .../mageck/test/tests/main.nf.test.snap | 142 +++++++++++------- .../test/tests/nextflow-day0_label.config | 6 - .../nf-core/mageck/test/tests/nextflow.config | 2 +- 14 files changed, 294 insertions(+), 273 deletions(-) delete mode 100644 modules/nf-core/mageck/test/tests/nextflow-day0_label.config diff --git a/modules/nf-core/mageck/count/main.nf b/modules/nf-core/mageck/count/main.nf index 596292dbbf44..ed822902ca3f 100644 --- a/modules/nf-core/mageck/count/main.nf +++ b/modules/nf-core/mageck/count/main.nf @@ -12,9 +12,9 @@ process MAGECK_COUNT { path(library) output: - tuple val(meta), path("*count.txt") , emit: count + tuple val(meta), path("*count.txt") , emit: count tuple val(meta), path("*.count_normalized.txt"), emit: norm - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("mageck"), eval("mageck -v"), emit: versions_mageck, topic: versions when: task.ext.when == null || task.ext.when @@ -22,32 +22,22 @@ process MAGECK_COUNT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input_file = ("$inputfile".endsWith(".fastq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}" - def sample_label = ("$inputfile".endsWith(".fastq.gz") || "$inputfile".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : '' + def input_file = ("${inputfile}".endsWith(".fastq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}" + def sample_label = ("${inputfile}".endsWith(".fastq.gz") || "${inputfile}".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : '' """ mageck \\ count \\ - $args \\ - -l $library \\ - -n $prefix \\ - $sample_label \\ - $input_file \\ - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS + ${args} \\ + -l ${library} \\ + -n ${prefix} \\ + ${sample_label} \\ + ${input_file} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.count.txt touch ${prefix}.count_normalized.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS """ } diff --git a/modules/nf-core/mageck/count/meta.yml b/modules/nf-core/mageck/count/meta.yml index fa4fa872dce7..6637449cb80b 100644 --- a/modules/nf-core/mageck/count/meta.yml +++ b/modules/nf-core/mageck/count/meta.yml @@ -1,6 +1,6 @@ name: "mageck_count" -description: mageck count for functional genomics, reads are usually mapped to a specific - sgRNA +description: mageck count for functional genomics, reads are usually mapped to a + specific sgRNA keywords: - sort - functional genomics @@ -13,7 +13,8 @@ tools: homepage: "https://sourceforge.net/p/mageck/wiki/Home/" documentation: "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command" doi: "10.1186/s13059-014-0554-4" - licence: ["BSD License"] + licence: + - "BSD License" identifier: biotools:mageck input: - - meta: @@ -23,8 +24,8 @@ input: e.g. [ id:'test', single_end:false ] - inputfile: type: file - description: library fastq file containing the sgRNA and gene name or count - table containing the sgRNA and number of reads to per sample + description: library fastq file containing the sgRNA and gene name or + count table containing the sgRNA and number of reads to per sample pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" ontologies: - edam: http://edamontology.org/format_1930 # FASTQ @@ -60,13 +61,29 @@ output: description: File containing normalized read counts pattern: "*.count_normalized.txt" ontologies: [] + versions_mageck: + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/count/tests/main.nf.test b/modules/nf-core/mageck/count/tests/main.nf.test index fbfeaeb641f6..504e69280e8f 100644 --- a/modules/nf-core/mageck/count/tests/main.nf.test +++ b/modules/nf-core/mageck/count/tests/main.nf.test @@ -14,9 +14,12 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test,test2', single_end:true] , // meta map - [file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)] + input[0] = [ + [ id:'test,test2' ], + [ + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true) + ] ] input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv') """ @@ -26,7 +29,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -39,9 +42,12 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test,test2', single_end:true] , // meta map - [file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)] + input[0] = [ + [ id:'test,test2' ], + [ + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true) + ] ] input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv') """ @@ -51,8 +57,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/mageck/count/tests/main.nf.test.snap b/modules/nf-core/mageck/count/tests/main.nf.test.snap index 31dbc74b4ab6..db85cabfbdbe 100644 --- a/modules/nf-core/mageck/count/tests/main.nf.test.snap +++ b/modules/nf-core/mageck/count/tests/main.nf.test.snap @@ -2,32 +2,10 @@ "mus_musculus - fastq": { "content": [ { - "0": [ - [ - { - "id": "test,test2", - "single_end": true - }, - "test,test2.count.txt:md5,2759bdc010998f863518cf7a2df812dc" - ] - ], - "1": [ - [ - { - "id": "test,test2", - "single_end": true - }, - "test,test2.count_normalized.txt:md5,d79f3863168ee0f0750a59d94f70ce1a" - ] - ], - "2": [ - "versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9" - ], "count": [ [ { - "id": "test,test2", - "single_end": true + "id": "test,test2" }, "test,test2.count.txt:md5,2759bdc010998f863518cf7a2df812dc" ] @@ -35,48 +13,33 @@ "norm": [ [ { - "id": "test,test2", - "single_end": true + "id": "test,test2" }, "test,test2.count_normalized.txt:md5,d79f3863168ee0f0750a59d94f70ce1a" ] ], - "versions": [ - "versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9" + "versions_mageck": [ + [ + "MAGECK_COUNT", + "mageck", + "0.5.9.5" + ] ] } ], - "timestamp": "2024-06-14T17:31:00.990366" + "timestamp": "2026-06-19T14:46:05.983468802", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "mus_musculus - fastq - stub": { "content": [ { - "0": [ - [ - { - "id": "test,test2", - "single_end": true - }, - "test,test2.count.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test,test2", - "single_end": true - }, - "test,test2.count_normalized.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9" - ], "count": [ [ { - "id": "test,test2", - "single_end": true + "id": "test,test2" }, "test,test2.count.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -84,17 +47,24 @@ "norm": [ [ { - "id": "test,test2", - "single_end": true + "id": "test,test2" }, "test,test2.count_normalized.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9" + "versions_mageck": [ + [ + "MAGECK_COUNT", + "mageck", + "0.5.9.5" + ] ] } ], - "timestamp": "2024-06-14T17:31:12.173269" + "timestamp": "2026-06-19T14:46:14.042271757", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/mageck/mle/main.nf b/modules/nf-core/mageck/mle/main.nf index ba119c29a8b6..3591d0b5a4c5 100644 --- a/modules/nf-core/mageck/mle/main.nf +++ b/modules/nf-core/mageck/mle/main.nf @@ -14,7 +14,7 @@ process MAGECK_MLE { output: tuple val(meta), path("*.gene_summary.txt") , emit: gene_summary tuple val(meta), path("*.sgrna_summary.txt"), emit: sgrna_summary - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("mageck"), eval("mageck -v"), emit: versions_mageck, topic: versions when: task.ext.when == null || task.ext.when @@ -26,16 +26,11 @@ process MAGECK_MLE { """ mageck \\ mle \\ - $args \\ - --threads $task.cpus \\ - -k $count_table \\ - -d $design_matrix \\ - -n $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS + ${args} \\ + --threads ${task.cpus} \\ + -k ${count_table} \\ + -d ${design_matrix} \\ + -n ${prefix} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" @@ -43,11 +38,6 @@ process MAGECK_MLE { """ touch ${prefix}.gene_summary.txt touch ${prefix}.sgrna_summary.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS """ diff --git a/modules/nf-core/mageck/mle/meta.yml b/modules/nf-core/mageck/mle/meta.yml index 59fb5b7f622b..590e424585b5 100644 --- a/modules/nf-core/mageck/mle/meta.yml +++ b/modules/nf-core/mageck/mle/meta.yml @@ -12,7 +12,8 @@ tools: documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" - licence: ["BSD"] + licence: + - "BSD" identifier: biotools:mageck input: - - meta: @@ -63,13 +64,29 @@ output: associated gene pattern: "*.{gene_summary}" ontologies: [] + versions_mageck: + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/mle/tests/main.nf.test b/modules/nf-core/mageck/mle/tests/main.nf.test index f6d06280485f..69791dbc8a38 100644 --- a/modules/nf-core/mageck/mle/tests/main.nf.test +++ b/modules/nf-core/mageck/mle/tests/main.nf.test @@ -15,11 +15,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] - input[1] = - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) """ } } @@ -27,11 +26,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, { assert file(process.out.gene_summary[0][1]).readLines().first().contains("Gene") }, - { assert file(process.out.sgrna_summary[0][1]).exists() } - ) - + { assert snapshot(sanitizeOutput(process.out, unstableKeys:["gene_summary"])).match() } + ) } } @@ -44,11 +41,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] - input[1] = - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) """ } } @@ -56,7 +52,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/mageck/mle/tests/main.nf.test.snap b/modules/nf-core/mageck/mle/tests/main.nf.test.snap index 6fb2101d8046..5e05ff2cdcf0 100644 --- a/modules/nf-core/mageck/mle/tests/main.nf.test.snap +++ b/modules/nf-core/mageck/mle/tests/main.nf.test.snap @@ -2,66 +2,69 @@ "mageck_mle - csv - stub": { "content": [ { - "0": [ + "gene_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.gene_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "1": [ + "sgrna_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.sgrna_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ - "versions.yml:md5,d83f4ee1ef0e972c5ea9a8deee7ba3b3" - ], + "versions_mageck": [ + [ + "MAGECK_MLE", + "mageck", + "0.5.9.5" + ] + ] + } + ], + "timestamp": "2026-06-19T14:40:48.942740107", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "mageck_mle - csv": { + "content": [ + { "gene_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.gene_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.gene_summary.txt" ] ], "sgrna_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.sgrna_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.sgrna_summary.txt:md5,2d9c7b762ca4086f6d84a869f0961f3b" ] ], - "versions": [ - "versions.yml:md5,d83f4ee1ef0e972c5ea9a8deee7ba3b3" + "versions_mageck": [ + [ + "MAGECK_MLE", + "mageck", + "0.5.9.5" + ] ] } ], + "timestamp": "2026-06-19T14:52:49.990501703", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-04T13:27:46.709493836" - }, - "mageck_mle - csv": { - "content": [ - [ - "versions.yml:md5,d83f4ee1ef0e972c5ea9a8deee7ba3b3" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-04T10:55:23.297715246" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/mageck/test/main.nf b/modules/nf-core/mageck/test/main.nf index 2e16d7b07b53..713c3f0a8588 100644 --- a/modules/nf-core/mageck/test/main.nf +++ b/modules/nf-core/mageck/test/main.nf @@ -14,7 +14,7 @@ process MAGECK_TEST { tuple val(meta), path("*.gene_summary.txt") , emit: gene_summary tuple val(meta), path("*.sgrna_summary.txt") , emit: sgrna_summary tuple val(meta), path("*.R") , emit: r_script, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("mageck"), eval("mageck -v"), emit: versions_mageck, topic: versions when: task.ext.when == null || task.ext.when @@ -29,11 +29,6 @@ process MAGECK_TEST { $args \\ -k $count_table \\ -n $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS """ stub: @@ -42,10 +37,5 @@ process MAGECK_TEST { touch ${prefix}.gene_summary.txt touch ${prefix}.sgrna_summary.txt touch ${prefix}.R - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mageck: \$(mageck -v) - END_VERSIONS """ } diff --git a/modules/nf-core/mageck/test/meta.yml b/modules/nf-core/mageck/test/meta.yml index 7c5109f094d4..066d0f3ce8a4 100644 --- a/modules/nf-core/mageck/test/meta.yml +++ b/modules/nf-core/mageck/test/meta.yml @@ -1,6 +1,6 @@ name: "mageck_test" -description: Mageck test performs a robust ranking aggregation (RRA) to identify positively - or negatively selected genes in functional genomics screens. +description: Mageck test performs a robust ranking aggregation (RRA) to identify + positively or negatively selected genes in functional genomics screens. keywords: - sort - rra @@ -13,7 +13,8 @@ tools: documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" - licence: ["BSD License"] + licence: + - "BSD License" identifier: biotools:mageck input: - - meta: @@ -72,13 +73,29 @@ output: pattern: "*.R" ontologies: - edam: http://edamontology.org/format_3999 # R script + versions_mageck: + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - mageck: + type: string + description: The name of the tool + - mageck -v: + type: eval + description: The expression to obtain the version of the tool + authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/test/tests/main.nf.test b/modules/nf-core/mageck/test/tests/main.nf.test index 45cb37345f6c..04325946431d 100644 --- a/modules/nf-core/mageck/test/tests/main.nf.test +++ b/modules/nf-core/mageck/test/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process MAGECK_TEST" script "../main.nf" + config "./nextflow.config" process "MAGECK_TEST" tag "modules" @@ -10,15 +11,16 @@ nextflow_process { tag "mageck/test" test("mageck-test - csv") { - - config "./nextflow.config" - when { + params { + module_args = "-t 'HL60.initial' " + } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) - ] + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) + ] """ } } @@ -26,28 +28,23 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.gene_summary.get(0).get(1)).readLines()[0], - file(process.out.sgrna_summary.get(0).get(1)).readLines()[0], - file(process.out.r_script.get(0).get(1)).readLines()[0] - ).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } test("mageck-test-day0 - csv") { - - config "./nextflow-day0_label.config" - when { + params { + module_args = "--day0-label 'HL60.initial' " + } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) - ] + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) + ] """ } } @@ -55,12 +52,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.gene_summary.get(0).get(1)[0]).readLines()[0], - file(process.out.sgrna_summary.get(0).get(1)[0]).readLines()[0] - ).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -71,11 +63,15 @@ nextflow_process { options "-stub" when { + params { + module_args = "" + } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) - ] + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) + ] """ } } @@ -83,7 +79,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/mageck/test/tests/main.nf.test.snap b/modules/nf-core/mageck/test/tests/main.nf.test.snap index 3b69c697fd54..a6dc8a98eb7e 100644 --- a/modules/nf-core/mageck/test/tests/main.nf.test.snap +++ b/modules/nf-core/mageck/test/tests/main.nf.test.snap @@ -2,101 +2,137 @@ "mageck-test - csv - stub": { "content": [ { - "0": [ + "gene_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.gene_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "1": [ + "r_script": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.sgrna_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.R:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ + "sgrna_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.R:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.sgrna_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ - "versions.yml:md5,d63cf999d719137c7310a3f5b4e03fd8" - ], + "versions_mageck": [ + [ + "MAGECK_TEST", + "mageck", + "0.5.9.5" + ] + ] + } + ], + "timestamp": "2026-06-19T14:43:43.267128486", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "mageck-test - csv": { + "content": [ + { "gene_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.gene_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.gene_summary.txt:md5,23d39164e44e7125a5f5912463fa5970" ] ], "r_script": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.R:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.R:md5,9c913f55aa7e7142399396088332ea3b" ] ], "sgrna_summary": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test.sgrna_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.sgrna_summary.txt:md5,26e4a50272a0289b0261a5380276f273" ] ], - "versions": [ - "versions.yml:md5,d63cf999d719137c7310a3f5b4e03fd8" + "versions_mageck": [ + [ + "MAGECK_TEST", + "mageck", + "0.5.9.5" + ] ] } ], + "timestamp": "2026-06-19T14:58:18.071931034", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.07.0" - }, - "timestamp": "2024-06-17T15:11:41.655784" - }, - "mageck-test - csv": { - "content": [ - [ - "versions.yml:md5,d63cf999d719137c7310a3f5b4e03fd8" - ], - "id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc", - "sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment", - "pdf(file='test.pdf',width=4.5,height=4.5);" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.07.0" - }, - "timestamp": "2024-06-17T15:11:06.123141" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "mageck-test-day0 - csv": { "content": [ - [ - "versions.yml:md5,d63cf999d719137c7310a3f5b4e03fd8" - ], - "id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc", - "sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment" + { + "gene_summary": [ + [ + { + "id": "test" + }, + [ + "test.HL60.final_vs_HL60.initial.gene_summary.txt:md5,973d57a2a432eb6c7e602ca466299b6d", + "test.KBM7.final_vs_HL60.initial.gene_summary.txt:md5,5a39c0132560cf6a3818b0e463df99a9", + "test.KBM7.initial_vs_HL60.initial.gene_summary.txt:md5,d532a4280945d28bad2186287b32cb3e", + "test.gene_summary.txt:md5,2e5447f5930f01f9adea57bf89cec5fe" + ] + ] + ], + "r_script": [ + [ + { + "id": "test" + }, + "test.R:md5,0849644a8ebfef2cf35d1ac351a02bca" + ] + ], + "sgrna_summary": [ + [ + { + "id": "test" + }, + [ + "test.HL60.final_vs_HL60.initial.sgrna_summary.txt:md5,a299a0f2cf7ce62bcf8aa4b4f48ea9db", + "test.KBM7.final_vs_HL60.initial.sgrna_summary.txt:md5,aeb64ee78422ef4906161cb03c0c0ad2", + "test.KBM7.initial_vs_HL60.initial.sgrna_summary.txt:md5,60c9104cad7d49bcead4d29cafb2af40", + "test.sgrna_summary.txt:md5,60c9104cad7d49bcead4d29cafb2af40" + ] + ] + ], + "versions_mageck": [ + [ + "MAGECK_TEST", + "mageck", + "0.5.9.5" + ] + ] + } ], + "timestamp": "2026-06-19T14:58:31.303470713", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.07.0" - }, - "timestamp": "2024-06-17T15:11:25.915572" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/mageck/test/tests/nextflow-day0_label.config b/modules/nf-core/mageck/test/tests/nextflow-day0_label.config deleted file mode 100644 index 4a33e5fb2eba..000000000000 --- a/modules/nf-core/mageck/test/tests/nextflow-day0_label.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - withName: 'MAGECK_TEST' { - ext.args = "--day0-label 'HL60.initial' " - } -} diff --git a/modules/nf-core/mageck/test/tests/nextflow.config b/modules/nf-core/mageck/test/tests/nextflow.config index 48f875850a5b..573b98d61d26 100644 --- a/modules/nf-core/mageck/test/tests/nextflow.config +++ b/modules/nf-core/mageck/test/tests/nextflow.config @@ -1,6 +1,6 @@ process { withName: 'MAGECK_TEST' { - ext.args = "-t 'HL60.initial' " + ext.args = params.module_args } }