diff --git a/modules/nf-core/perbase/environment.yml b/modules/nf-core/perbase/environment.yml index 041d6bfdb1e7..eefde32a822d 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=1.4.0 diff --git a/modules/nf-core/perbase/main.nf b/modules/nf-core/perbase/main.nf index 8547e0883532..3df9fd5b25d4 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/fd/fd166ca25d396f7558faf94f3b9b508bc73379181c29dc7c134d5b4a29109a81/data': + 'community.wave.seqera.io/library/perbase:1.4.0--9d769b8ba6979df2' }" 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 @@ -33,21 +33,11 @@ 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: 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..5eeb68543319 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" @@ -72,14 +71,29 @@ output: ontologies: - edam: "http://edamontology.org/format_3475" + 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: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + - - ${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 - ontologies: - - edam: http://edamontology.org/format_3750 # YAML 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..6b622584fa12 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:md5,6619c230abd5af642f0bb5dd4bedbd2f" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -20,19 +24,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,a18ee6e481ab7cbad3c3a9f71465b904" + "test.tsv.gz:md5,6619c230abd5af642f0bb5dd4bedbd2f" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:16:11.391508924" }, "homo_sapiens - illumina - bam, bai, []": { "content": [ @@ -43,11 +51,15 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,e172f00dfb22f5b09a359e011021a85b" + "test.tsv.gz:md5,7b04495cbdee506e402bcacc01f88a2a" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -55,19 +67,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,e172f00dfb22f5b09a359e011021a85b" + "test.tsv.gz:md5,7b04495cbdee506e402bcacc01f88a2a" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:15:41.822723156" }, "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,d7df42c2774129a25ae84a29e02f938b" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -90,19 +110,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,587c451b76aa1c0c23416f8590f146fa" + "test.tsv.gz:md5,d7df42c2774129a25ae84a29e02f938b" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:16:43.015464065" }, "homo_sapiens - illumina - cram, crai, fasta, fai, [] - stub": { "content": [ @@ -117,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -128,16 +156,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:15:28.393905034" }, "homo_sapiens - illumina - bam, bai, [] - stub": { "content": [ @@ -152,7 +184,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -163,16 +199,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:15:54.612458251" }, "homo_sapiens - illumina - bam, bai, bed - stub": { "content": [ @@ -187,7 +227,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -198,16 +242,20 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:16:59.025003686" }, "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,f5f1035e4296fd299dc47947fa0b4c01" ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -230,19 +282,23 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,4891d953dec9a74fe2ab34042724f929" + "test.tsv.gz:md5,f5f1035e4296fd299dc47947fa0b4c01" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:15:17.938018267" }, "homo_sapiens - illumina - cram, crai, fasta, fai, bed - stub": { "content": [ @@ -257,7 +313,11 @@ ] ], "1": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + [ + "PERBASE", + "perbase", + "1.4.0" + ] ], "tsv": [ [ @@ -268,15 +328,19 @@ "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,176428b3d32243a2ec5f37649d79703c" + "versions_perbase": [ + [ + "PERBASE", + "perbase", + "1.4.0" + ] ] } ], "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": "2026-02-06T14:16:25.613409317" } } \ No newline at end of file