From 7a444cb9bb2c8befdb9abecb177d4fd568ae9114 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Fri, 17 Jul 2026 11:13:55 +0200 Subject: [PATCH 1/3] migrate to version topic --- .../sequencetools/pileupcaller/main.nf | 12 +--- .../sequencetools/pileupcaller/meta.yml | 61 +++++++++++-------- 2 files changed, 38 insertions(+), 35 deletions(-) diff --git a/modules/nf-core/sequencetools/pileupcaller/main.nf b/modules/nf-core/sequencetools/pileupcaller/main.nf index 169860a8fc47..a47b46561638 100644 --- a/modules/nf-core/sequencetools/pileupcaller/main.nf +++ b/modules/nf-core/sequencetools/pileupcaller/main.nf @@ -16,7 +16,7 @@ process SEQUENCETOOLS_PILEUPCALLER { tuple val(meta), path("*.geno"), path("*.snp"), path("*.ind"), emit: eigenstrat, optional:true tuple val(meta), path("*.bed") , path("*.bim"), path("*.fam"), emit: plink , optional:true tuple val(meta), path("*.freqsum.gz") , emit: freqsum , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("sequencetools"), eval("pileupCaller --version 2>&1"), topic: versions, emit: versions_pileupcaller when: task.ext.when == null || task.ext.when @@ -36,11 +36,6 @@ process SEQUENCETOOLS_PILEUPCALLER { ${sample_names} \\ ${args} \\ ${freqsum_output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sequencetools: \$(echo \$(pileupCaller --version 2>&1) ) - END_VERSIONS """ stub: @@ -55,10 +50,5 @@ process SEQUENCETOOLS_PILEUPCALLER { ${freqsum_output} ${plink_output} ${eigenstrat_output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sequencetools: \$(echo \$(pileupCaller --version 2>&1) ) - END_VERSIONS """ } diff --git a/modules/nf-core/sequencetools/pileupcaller/meta.yml b/modules/nf-core/sequencetools/pileupcaller/meta.yml index 2fbdb240a315..b3fd68f449b0 100644 --- a/modules/nf-core/sequencetools/pileupcaller/meta.yml +++ b/modules/nf-core/sequencetools/pileupcaller/meta.yml @@ -1,6 +1,6 @@ name: "sequencetools_pileupcaller" -description: PileupCaller is a tool to create genotype calls from bam files using - read-sampling methods +description: PileupCaller is a tool to create genotype calls from bam files + using read-sampling methods keywords: - genotyping - mpileup @@ -17,10 +17,10 @@ tools: homepage: "https://github.com/stschiff/sequenceTools" documentation: "https://github.com/stschiff/sequenceTools#readme" tool_dev_url: "https://github.com/stschiff/sequenceTools" - licence: ["MIT"] + licence: + - "MIT" identifier: "" input: - # Only when we have meta - - meta: type: map description: | @@ -41,7 +41,6 @@ input: description: File containing the sample names ontologies: [] output: - #Only when we have meta eigenstrat: - - meta: type: map @@ -50,20 +49,20 @@ output: e.g. [ id:'test', single_end:false ] - "*.geno": type: file - description: A tuple containing the output Eigenstrat-formatted geno, snp - and ind files. + description: A tuple containing the output Eigenstrat-formatted geno, + snp and ind files. pattern: "*.{geno,snp,ind}.txt" ontologies: [] - "*.snp": type: file - description: A tuple containing the output Eigenstrat-formatted geno, snp - and ind files. + description: A tuple containing the output Eigenstrat-formatted geno, + snp and ind files. pattern: "*.{geno,snp,ind}.txt" ontologies: [] - "*.ind": type: file - description: A tuple containing the output Eigenstrat-formatted geno, snp - and ind files. + description: A tuple containing the output Eigenstrat-formatted geno, + snp and ind files. pattern: "*.{geno,snp,ind}.txt" ontologies: [] plink: @@ -74,20 +73,20 @@ output: e.g. [ id:'test', single_end:false ] - "*.bed": type: file - description: A tuple containing the output Plink-formatted bed, bim and fam - files. + description: A tuple containing the output Plink-formatted bed, bim and + fam files. pattern: "*.{bed,bim,fam}" ontologies: [] - "*.bim": type: file - description: A tuple containing the output Plink-formatted bed, bim and fam - files. + description: A tuple containing the output Plink-formatted bed, bim and + fam files. pattern: "*.{bed,bim,fam}" ontologies: [] - "*.fam": type: file - description: A tuple containing the output Plink-formatted bed, bim and fam - files. + description: A tuple containing the output Plink-formatted bed, bim and + fam files. pattern: "*.{bed,bim,fam}" ontologies: [] freqsum: @@ -101,14 +100,28 @@ output: description: The output freqsum-formatted file. pattern: "*.freqsum.gz" ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 + versions_pileupcaller: + - - ${task.process}: + type: string + description: The name of the process + - sequencetools: + type: string + description: The name of the tool + - pileupCaller --version 2>&1: + 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 + - sequencetools: + type: string + description: The name of the tool + - pileupCaller --version 2>&1: + type: eval + description: The expression to obtain the version of the tool authors: - "@TCLamnidis" maintainers: From 88e6495478b7fafba0bb71083b54fb1031439510 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Mon, 20 Jul 2026 15:21:46 +0200 Subject: [PATCH 2/3] Update nf-test and snapshots --- .../pileupcaller/tests/main.nf.test | 3 - .../pileupcaller/tests/main.nf.test.snap | 73 ++++++++----------- 2 files changed, 30 insertions(+), 46 deletions(-) diff --git a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test index 1b35e45ea2f1..0af2806a7fd1 100644 --- a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test +++ b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test @@ -31,7 +31,6 @@ nextflow_process { { assert snapshot( path(process.out.freqsum[0][1]).linesGzip[0..4], process.out.versions, - path(process.out.versions[0]).yaml ).match() } ) } @@ -60,7 +59,6 @@ nextflow_process { process.out.eigenstrat[0][2], process.out.eigenstrat[0][3], process.out.versions, - path(process.out.versions[0]).yaml ).match() } ) } @@ -89,7 +87,6 @@ nextflow_process { process.out.plink[0][2], process.out.plink[0][3], process.out.versions, - path(process.out.versions[0]).yaml ).match() } ) } diff --git a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap index a7055c84ab34..0aabdddd3b28 100644 --- a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap +++ b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap @@ -4,20 +4,13 @@ "test.geno", "test.snp:md5,1c64da4b67bbc46ea4ac3146efb37346", "test.ind:md5,f8d5d94b39e3693452af54688649aaad", - [ - "versions.yml:md5,2ce04439173fcba8671d312e79f3a148" - ], - { - "SEQUENCETOOLS_PILEUPCALLER": { - "sequencetools": "1.6.0.0" - } - } + null ], + "timestamp": "2026-07-20T14:44:40.60236", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-23T10:48:45.195842" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "freqsum - stub": { "content": [ @@ -37,7 +30,11 @@ ] ], "3": [ - "versions.yml:md5,2ce04439173fcba8671d312e79f3a148" + [ + "SEQUENCETOOLS_PILEUPCALLER", + "sequencetools", + "1.6.0.0" + ] ], "eigenstrat": [ @@ -53,36 +50,33 @@ "plink": [ ], - "versions": [ - "versions.yml:md5,2ce04439173fcba8671d312e79f3a148" + "versions_pileupcaller": [ + [ + "SEQUENCETOOLS_PILEUPCALLER", + "sequencetools", + "1.6.0.0" + ] ] } ], + "timestamp": "2026-07-20T14:40:00.956534", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-23T09:23:25.707102" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "plink": { "content": [ "test.bed", "test.bim:md5,4618dec3be68386e18562a3f4812e0dc", "test.fam:md5,f3e98d680273a975b00ea6e0d67cfad1", - [ - "versions.yml:md5,2ce04439173fcba8671d312e79f3a148" - ], - { - "SEQUENCETOOLS_PILEUPCALLER": { - "sequencetools": "1.6.0.0" - } - } + null ], + "timestamp": "2026-07-20T14:45:07.644069", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-23T10:49:59.522249" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } }, "freqsum": { "content": [ @@ -93,19 +87,12 @@ "21\t11002011\tT\tC\t-1", "21\t14601415\tG\tA\t-1" ], - [ - "versions.yml:md5,2ce04439173fcba8671d312e79f3a148" - ], - { - "SEQUENCETOOLS_PILEUPCALLER": { - "sequencetools": "1.6.0.0" - } - } + null ], + "timestamp": "2026-07-20T14:44:13.869361", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-23T21:11:12.666134" + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } } } \ No newline at end of file From 063ab74990c8dbc689e5f4a03c6d2191bdca63bb Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Mon, 20 Jul 2026 15:48:19 +0200 Subject: [PATCH 3/3] update test and snapshot. Thanks @mashehu --- .../pileupcaller/tests/main.nf.test | 6 +-- .../pileupcaller/tests/main.nf.test.snap | 38 +++++++++++++++---- 2 files changed, 34 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test index 0af2806a7fd1..76f921850f64 100644 --- a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test +++ b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { assertAll( { assert snapshot( path(process.out.freqsum[0][1]).linesGzip[0..4], - process.out.versions, + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) } @@ -58,7 +58,7 @@ nextflow_process { file(process.out.eigenstrat[0][1]).name, process.out.eigenstrat[0][2], process.out.eigenstrat[0][3], - process.out.versions, + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) } @@ -86,7 +86,7 @@ nextflow_process { file(process.out.plink[0][1]).name, process.out.plink[0][2], process.out.plink[0][3], - process.out.versions, + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) } diff --git a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap index 0aabdddd3b28..5335d32ca378 100644 --- a/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap +++ b/modules/nf-core/sequencetools/pileupcaller/tests/main.nf.test.snap @@ -4,9 +4,17 @@ "test.geno", "test.snp:md5,1c64da4b67bbc46ea4ac3146efb37346", "test.ind:md5,f8d5d94b39e3693452af54688649aaad", - null + { + "versions_pileupcaller": [ + [ + "SEQUENCETOOLS_PILEUPCALLER", + "sequencetools", + "1.6.0.0" + ] + ] + } ], - "timestamp": "2026-07-20T14:44:40.60236", + "timestamp": "2026-07-20T15:43:48.322784", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" @@ -59,7 +67,7 @@ ] } ], - "timestamp": "2026-07-20T14:40:00.956534", + "timestamp": "2026-07-20T15:44:21.402431", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" @@ -70,9 +78,17 @@ "test.bed", "test.bim:md5,4618dec3be68386e18562a3f4812e0dc", "test.fam:md5,f3e98d680273a975b00ea6e0d67cfad1", - null + { + "versions_pileupcaller": [ + [ + "SEQUENCETOOLS_PILEUPCALLER", + "sequencetools", + "1.6.0.0" + ] + ] + } ], - "timestamp": "2026-07-20T14:45:07.644069", + "timestamp": "2026-07-20T15:44:13.398562", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4" @@ -87,9 +103,17 @@ "21\t11002011\tT\tC\t-1", "21\t14601415\tG\tA\t-1" ], - null + { + "versions_pileupcaller": [ + [ + "SEQUENCETOOLS_PILEUPCALLER", + "sequencetools", + "1.6.0.0" + ] + ] + } ], - "timestamp": "2026-07-20T14:44:13.869361", + "timestamp": "2026-07-20T15:43:22.87245", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.4"