diff --git a/modules/nf-core/cnvpytor/importreaddepth/environment.yml b/modules/nf-core/cnvpytor/importreaddepth/environment.yml index abf3155006b8..64ff86280b00 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/environment.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::cnvpytor=1.3.1 - - conda-forge::numpy=1.24.3 + - bioconda::cnvpytor=1.3.2 + - conda-forge::make=4.4.1 diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 1238a48f19f1..0a73b570a867 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -4,8 +4,8 @@ process CNVPYTOR_IMPORTREADDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.3.1--pyhdfd78af_1': - 'biocontainers/cnvpytor:1.3.1--pyhdfd78af_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bbb6343edff4191cb1f445b2aac028d1f805ed5a7d50799513c82531bcfdede5/data': + 'community.wave.seqera.io/library/cnvpytor_make:a8fdcebe82041114' }" input: tuple val(meta), path(input_file), path(index) @@ -14,7 +14,11 @@ process CNVPYTOR_IMPORTREADDEPTH { output: tuple val(meta), path("*.pytor") , emit: pytor - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('cnvpytor'), val('1.3.2'), emit: versions_cnvpytor, topic: versions + // cnvpytor version is hardcoded due to this error when calling cnvpytor --version + // > cnvpytor --version + // 2026-03-13 16:14:08,088 - cnvpytor - ERROR - Some reference genome resource files are missing. + // Run 'cnvpytor -download' as same user who has installed cnvpytor. when: task.ext.when == null || task.ext.when @@ -29,21 +33,11 @@ process CNVPYTOR_IMPORTREADDEPTH { -rd $input_file \\ $args \\ $reference - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvpytor: \$(cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.pytor - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvpytor: \$(cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p') - END_VERSIONS """ } diff --git a/modules/nf-core/cnvpytor/importreaddepth/meta.yml b/modules/nf-core/cnvpytor/importreaddepth/meta.yml index 93a111801fb5..aa2e960af9a1 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/meta.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/meta.yml @@ -1,6 +1,6 @@ name: cnvpytor_importreaddepth -description: command line tool for CNV/CNA analysis. This step imports the read depth - data into a root pytor file. +description: command line tool for CNV/CNA analysis. This step imports the read + depth data into a root pytor file. keywords: - read depth - cnv @@ -13,7 +13,8 @@ tools: documentation: https://github.com/abyzovlab/CNVpytor tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:cnvpytor input: - - meta: @@ -33,8 +34,8 @@ input: ontologies: [] - fasta: type: file - description: specifies reference genome file (only for cram file without reference - genome) + description: specifies reference genome file (only for cram file without + reference genome) pattern: "*.{fasta,fasta.gz,fa,fa.gz}" ontologies: [] - fai: @@ -51,17 +52,31 @@ output: e.g. [ id:'test' ] - "*.pytor": type: file - description: read depth root file in which read depth data binned to 100 base - pair bins will be stored. + description: read depth root file in which read depth data binned to 100 + base pair bins will be stored. pattern: "*.{pytor}" ontologies: [] + versions_cnvpytor: + - - ${task.process}: + type: string + description: The name of the process + - cnvpytor: + type: string + description: The name of the tool + - 1.3.2: + type: string + 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 + - cnvpytor: + type: string + description: The name of the tool + - 1.3.2: + type: string + description: The expression to obtain the version of the tool authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test index 316afecb1499..cc0f78ad8e7c 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test +++ b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.pytor[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) @@ -62,7 +62,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.pytor[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) diff --git a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test.snap b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test.snap index 0339e3824e3d..6483990685b4 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test.snap +++ b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test.snap @@ -2,15 +2,21 @@ "test-cnvpytor-importreaddepth": { "content": [ "test.pytor", - [ - "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27" - ] + { + "versions_cnvpytor": [ + [ + "CNVPYTOR_IMPORTREADDEPTH", + "cnvpytor", + "1.3.1" + ] + ] + } ], + "timestamp": "2026-03-13T13:08:50.744070399", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-28T14:03:16.865191" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-cnvpytor-importreaddepth-cram-stub": { "content": [ @@ -24,7 +30,11 @@ ] ], "1": [ - "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27" + [ + "CNVPYTOR_IMPORTREADDEPTH", + "cnvpytor", + "1.3.2" + ] ], "pytor": [ [ @@ -34,28 +44,38 @@ "test.pytor:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27" + "versions_cnvpytor": [ + [ + "CNVPYTOR_IMPORTREADDEPTH", + "cnvpytor", + "1.3.2" + ] ] } ], + "timestamp": "2026-03-13T16:34:42.62061788", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-28T14:03:34.286753" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-cnvpytor-importreaddepth-cram": { "content": [ "test.pytor", - [ - "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27" - ] + { + "versions_cnvpytor": [ + [ + "CNVPYTOR_IMPORTREADDEPTH", + "cnvpytor", + "1.3.1" + ] + ] + } ], + "timestamp": "2026-03-13T13:09:01.201749134", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-28T14:03:27.674852" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file