From 0676624bd6be06016f239d90a8c96c73ee406c7d Mon Sep 17 00:00:00 2001 From: Lorengol Date: Thu, 12 Mar 2026 21:28:00 +0000 Subject: [PATCH] module update version --- modules/nf-core/coverm/genome/main.nf | 12 +-- modules/nf-core/coverm/genome/meta.yml | 40 +++++---- .../coverm/genome/tests/main.nf.test.snap | 88 +++++++++++++------ 3 files changed, 85 insertions(+), 55 deletions(-) diff --git a/modules/nf-core/coverm/genome/main.nf b/modules/nf-core/coverm/genome/main.nf index 3d9a829faef8..ed3669658927 100644 --- a/modules/nf-core/coverm/genome/main.nf +++ b/modules/nf-core/coverm/genome/main.nf @@ -16,7 +16,7 @@ process COVERM_GENOME { output: tuple val(meta), path("*.tsv"), emit: coverage - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('coverm'), eval("coverm --version | sed 's/coverm //'"), emit: versions_coverm, topic: versions when: task.ext.when == null || task.ext.when @@ -45,21 +45,11 @@ process COVERM_GENOME { ${reference_str} \\ ${args} \\ --output-file ${prefix}.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coverm: \$(coverm --version | sed 's/coverm //') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coverm: \$(coverm --version | sed 's/coverm //') - END_VERSIONS """ } diff --git a/modules/nf-core/coverm/genome/meta.yml b/modules/nf-core/coverm/genome/meta.yml index 2891fa58b711..b5054357e3dd 100644 --- a/modules/nf-core/coverm/genome/meta.yml +++ b/modules/nf-core/coverm/genome/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "coverm_genome" description: Calculate read coverage per-genome keywords: @@ -14,16 +13,15 @@ tools: documentation: "https://wwood.github.io/CoverM/coverm-contig.html" tool_dev_url: "https://github.com/wwood/CoverM" doi: "10.5281/zenodo.10531253" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:coverm - input: - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - input: type: file description: | @@ -38,22 +36,19 @@ input: description: | Groovy Map containing reference information e.g. `[ id:'sample1', single_end:false ]` - - reference: type: file - description: Genome FASTA file(s) to map reads to, or a directory containing genome FASTA files. + description: Genome FASTA file(s) to map reads to, or a directory + containing genome FASTA files. pattern: "*.{fasta,fasta.gz,mmi,sti,fna,fna.gz,fa,fa.gz}" ontologies: - edam: http://edamontology.org/format_1929 # FASTA - - bam_input: type: boolean description: True if input is bam files - - interleaved: type: boolean description: True if input is interleaved fastq file - - ref_mode: type: string description: | @@ -63,7 +58,6 @@ input: - `"auto"`: Automatically detect based on whether the `reference` path is a directory or file. Defaults to `"auto"` if not provided. pattern: "^(dir|file|auto)$" - output: coverage: - - meta: @@ -79,13 +73,27 @@ output: pattern: "*.{tsv}" ontologies: - edam: http://edamontology.org/format_3475 # TSV + versions_coverm: + - - ${task.process}: + type: string + description: The name of the process + - coverm: + type: string + description: The name of the tool + - coverm --version | sed 's/coverm //': + 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 + - coverm: + type: string + description: The name of the tool + - coverm --version | sed 's/coverm //': + type: eval + description: The expression to obtain the version of the tool authors: - "@vinisalazar" maintainers: diff --git a/modules/nf-core/coverm/genome/tests/main.nf.test.snap b/modules/nf-core/coverm/genome/tests/main.nf.test.snap index 61ae6ddaa834..6c90d3a47041 100644 --- a/modules/nf-core/coverm/genome/tests/main.nf.test.snap +++ b/modules/nf-core/coverm/genome/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ], "coverage": [ [ @@ -23,16 +27,20 @@ "test.tsv:md5,60ac75e5dce5da12263fbeea80f9c7fa" ] ], - "versions": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + "versions_coverm": [ + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ] } ], + "timestamp": "2026-03-12T21:22:17.530293484", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-15T09:56:48.526382" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "coverm_genome - stub": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ], "coverage": [ [ @@ -58,16 +70,20 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + "versions_coverm": [ + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ] } ], + "timestamp": "2026-03-12T21:22:49.427370819", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-13T12:13:46.530094" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "coverm_genome - directory": { "content": [ @@ -82,7 +98,11 @@ ] ], "1": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ], "coverage": [ [ @@ -93,16 +113,20 @@ "test.tsv:md5,70b9ad4a4d90d9c6eb0ef4b52adaf636" ] ], - "versions": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + "versions_coverm": [ + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ] } ], + "timestamp": "2026-03-12T21:22:35.763864708", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-15T09:57:01.240803" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "coverm_genome - fastq": { "content": [ @@ -117,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ], "coverage": [ [ @@ -128,15 +156,19 @@ "test.tsv:md5,c16918076fbb85545cd0f29a228cb54f" ] ], - "versions": [ - "versions.yml:md5,dae5063ea283765643d819100103ae65" + "versions_coverm": [ + [ + "COVERM_GENOME", + "coverm", + "0.7.0" + ] ] } ], + "timestamp": "2026-03-12T21:22:09.909009391", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-15T09:56:44.561425" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file