diff --git a/modules/nf-core/perbase/environment.yml b/modules/nf-core/perbase/environment.yml index 041d6bfdb1e7..24d1d77daa73 100644 --- a/modules/nf-core/perbase/environment.yml +++ b/modules/nf-core/perbase/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::perbase=1.0.0 + - bioconda::perbase=1.2.0 diff --git a/modules/nf-core/perbase/main.nf b/modules/nf-core/perbase/main.nf index a40d7f12ff74..b066b0c829d6 100644 --- a/modules/nf-core/perbase/main.nf +++ b/modules/nf-core/perbase/main.nf @@ -4,8 +4,8 @@ process PERBASE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5fad22cc063bd389d2a62d7710721cac547aff657c37be0f7afb4a66420b66/data': - 'community.wave.seqera.io/library/perbase:1.0.0--913516700ed7b57e' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cbbc9b2585d5abbef69ca0b379353616e16c6b7b8aafdb0c8a2bee9c63747d8f/data': + 'community.wave.seqera.io/library/perbase:1.2.0--8d7275913f5d0463' }" input: tuple val(meta) , path(bam) , path(index), path(bed) @@ -13,7 +13,7 @@ process PERBASE { output: tuple val(meta), path("*.tsv.gz"), emit: tsv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('perbase'), eval('perbase --version |& sed "1!d ; s/perbase //"'), emit: versions_perbase, topic: versions when: task.ext.when == null || task.ext.when @@ -33,11 +33,6 @@ process PERBASE { --threads $task.cpus \\ --bgzip \\ --output ${prefix}.tsv.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - perbase: \$(perbase --version |& sed '1!d ; s/perbase //') - END_VERSIONS """ stub: @@ -45,10 +40,5 @@ process PERBASE { def prefix = task.ext.prefix ?: "${meta.id}" """ echo "" | gzip > ${prefix}.tsv.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - perbase: \$(perbase --version |& sed '1!d ; s/perbase //') - END_VERSIONS """ } diff --git a/modules/nf-core/perbase/meta.yml b/modules/nf-core/perbase/meta.yml index cd7845d54213..523f59b3c0e5 100644 --- a/modules/nf-core/perbase/meta.yml +++ b/modules/nf-core/perbase/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "perbase" description: Per-base metrics on BAM/CRAM files. keywords: @@ -37,8 +36,8 @@ input: - edam: "http://edamontology.org/format_3327" - bed: type: file - description: bed file containing regions of interest, where only bases - from the given regions will be reported + description: bed file containing regions of interest, where only bases from + the given regions will be reported pattern: "*.{bed}" ontologies: - edam: "http://edamontology.org/format_3003" @@ -80,6 +79,29 @@ output: ontologies: - edam: http://edamontology.org/format_3750 # YAML + versions_perbase: + - - ${task.process}: + type: string + description: The name of the process + - perbase: + type: string + description: The name of the tool + - perbase --version |& sed "1!d ; s/perbase //": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - perbase: + type: string + description: The name of the tool + - perbase --version |& sed "1!d ; s/perbase //": + type: eval + description: The expression to obtain the version of the tool + authors: - "@camlloyd" maintainers: diff --git a/modules/nf-core/perbase/tests/main.nf.test.snap b/modules/nf-core/perbase/tests/main.nf.test.snap index 99d158a5f822..06b0b960f3f0 100644 --- a/modules/nf-core/perbase/tests/main.nf.test.snap +++ b/modules/nf-core/perbase/tests/main.nf.test.snap @@ -8,11 +8,15 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,a18ee6e481ab7cbad3c3a9f71465b904" + "test.tsv.gz:md5,166c9660273811d344dac472ca935aae" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -20,19 +24,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,a18ee6e481ab7cbad3c3a9f71465b904" + "test.tsv.gz:md5,166c9660273811d344dac472ca935aae" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:31:19.235567463" + "timestamp": "2026-01-28T16:52:37.990335623" }, "homo_sapiens - illumina - bam, bai, []": { "content": [ @@ -43,11 +51,15 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,e172f00dfb22f5b09a359e011021a85b" + "test.tsv.gz:md5,32116805d79766c6cbef9fc84f8e983d" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -55,19 +67,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,e172f00dfb22f5b09a359e011021a85b" + "test.tsv.gz:md5,32116805d79766c6cbef9fc84f8e983d" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:30:49.831039308" + "timestamp": "2026-01-28T16:52:08.325486138" }, "homo_sapiens - illumina - bam, bai, bed": { "content": [ @@ -78,11 +94,15 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,587c451b76aa1c0c23416f8590f146fa" + "test.tsv.gz:md5,c8dde7a5a901a6c22e54e7f76a3b8687" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -90,19 +110,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,587c451b76aa1c0c23416f8590f146fa" + "test.tsv.gz:md5,c8dde7a5a901a6c22e54e7f76a3b8687" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:31:51.429460917" + "timestamp": "2026-01-28T16:53:10.311912656" }, "homo_sapiens - illumina - cram, crai, fasta, fai, [] - stub": { "content": [ @@ -117,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -128,16 +156,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:30:35.949188515" + "timestamp": "2026-01-28T16:51:54.219021092" }, "homo_sapiens - illumina - bam, bai, [] - stub": { "content": [ @@ -152,7 +184,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -163,16 +199,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:31:02.088702727" + "timestamp": "2026-01-28T16:52:20.791771125" }, "homo_sapiens - illumina - bam, bai, bed - stub": { "content": [ @@ -187,7 +227,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -198,16 +242,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:32:07.709733502" + "timestamp": "2026-01-28T16:53:26.068740315" }, "homo_sapiens - illumina - cram, crai, fasta, fai, []": { "content": [ @@ -218,11 +266,15 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,4891d953dec9a74fe2ab34042724f929" + "test.tsv.gz:md5,6d536dae721eb082f0ba0216f67a340f" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -230,19 +282,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,4891d953dec9a74fe2ab34042724f929" + "test.tsv.gz:md5,6d536dae721eb082f0ba0216f67a340f" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:30:25.591849045" + "timestamp": "2026-01-28T16:51:43.208109165" }, "homo_sapiens - illumina - cram, crai, fasta, fai, bed - stub": { "content": [ @@ -257,7 +313,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.2.0" + ] ], "tsv": [ [ @@ -268,15 +328,19 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-08-05T19:31:33.524248387" + "timestamp": "2026-01-28T16:52:52.730988602" } } \ No newline at end of file