From 698df2147c6afaad7f4ae31b6824e2144619206d Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Wed, 28 Jan 2026 16:58:46 +0000 Subject: [PATCH 1/6] Bump version in environment.yml --- modules/nf-core/perbase/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From d4265ec8866de1ad9f7c92de0720deb7afc56ef7 Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Wed, 28 Jan 2026 17:01:25 +0000 Subject: [PATCH 2/6] Bump version in container directive --- modules/nf-core/perbase/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/perbase/main.nf b/modules/nf-core/perbase/main.nf index a40d7f12ff74..7ae2a5c89b85 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) From 5856495943a63e29aff2f21b5c97339e370b59dd Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Wed, 28 Jan 2026 17:01:56 +0000 Subject: [PATCH 3/6] Use topic channels --- modules/nf-core/perbase/main.nf | 12 +- modules/nf-core/perbase/meta.yml | 28 ++- .../nf-core/perbase/tests/main.nf.test.snap | 176 ++++++++++++------ 3 files changed, 146 insertions(+), 70 deletions(-) diff --git a/modules/nf-core/perbase/main.nf b/modules/nf-core/perbase/main.nf index 7ae2a5c89b85..b066b0c829d6 100644 --- a/modules/nf-core/perbase/main.nf +++ b/modules/nf-core/perbase/main.nf @@ -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 From 26f4cbf676b69fd41c81ef57a69660591b0cf050 Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Fri, 6 Feb 2026 14:10:42 +0000 Subject: [PATCH 4/6] Bump perbase version to 1.4.0 --- modules/nf-core/perbase/environment.yml | 2 +- modules/nf-core/perbase/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/perbase/environment.yml b/modules/nf-core/perbase/environment.yml index 24d1d77daa73..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=1.2.0 + - bioconda::perbase=1.4.0 diff --git a/modules/nf-core/perbase/main.nf b/modules/nf-core/perbase/main.nf index b066b0c829d6..f0d0b2280757 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/cb/cbbc9b2585d5abbef69ca0b379353616e16c6b7b8aafdb0c8a2bee9c63747d8f/data': - 'community.wave.seqera.io/library/perbase:1.2.0--8d7275913f5d0463' }" + '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) From 3883f3f64352d81359e10a498508ee1f91a99ef3 Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Thu, 19 Feb 2026 10:45:00 +0000 Subject: [PATCH 5/6] Update snaps --- .../nf-core/perbase/tests/main.nf.test.snap | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/perbase/tests/main.nf.test.snap b/modules/nf-core/perbase/tests/main.nf.test.snap index 06b0b960f3f0..6b622584fa12 100644 --- a/modules/nf-core/perbase/tests/main.nf.test.snap +++ b/modules/nf-core/perbase/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,166c9660273811d344dac472ca935aae" + "test.tsv.gz:md5,6619c230abd5af642f0bb5dd4bedbd2f" ] ], "1": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -24,14 +24,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,166c9660273811d344dac472ca935aae" + "test.tsv.gz:md5,6619c230abd5af642f0bb5dd4bedbd2f" ] ], "versions_perbase": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -40,7 +40,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:52:37.990335623" + "timestamp": "2026-02-06T14:16:11.391508924" }, "homo_sapiens - illumina - bam, bai, []": { "content": [ @@ -51,14 +51,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,32116805d79766c6cbef9fc84f8e983d" + "test.tsv.gz:md5,7b04495cbdee506e402bcacc01f88a2a" ] ], "1": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -67,14 +67,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,32116805d79766c6cbef9fc84f8e983d" + "test.tsv.gz:md5,7b04495cbdee506e402bcacc01f88a2a" ] ], "versions_perbase": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -83,7 +83,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:52:08.325486138" + "timestamp": "2026-02-06T14:15:41.822723156" }, "homo_sapiens - illumina - bam, bai, bed": { "content": [ @@ -94,14 +94,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,c8dde7a5a901a6c22e54e7f76a3b8687" + "test.tsv.gz:md5,d7df42c2774129a25ae84a29e02f938b" ] ], "1": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -110,14 +110,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,c8dde7a5a901a6c22e54e7f76a3b8687" + "test.tsv.gz:md5,d7df42c2774129a25ae84a29e02f938b" ] ], "versions_perbase": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -126,7 +126,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:53:10.311912656" + "timestamp": "2026-02-06T14:16:43.015464065" }, "homo_sapiens - illumina - cram, crai, fasta, fai, [] - stub": { "content": [ @@ -144,7 +144,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -160,7 +160,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -169,7 +169,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:51:54.219021092" + "timestamp": "2026-02-06T14:15:28.393905034" }, "homo_sapiens - illumina - bam, bai, [] - stub": { "content": [ @@ -187,7 +187,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -203,7 +203,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -212,7 +212,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:52:20.791771125" + "timestamp": "2026-02-06T14:15:54.612458251" }, "homo_sapiens - illumina - bam, bai, bed - stub": { "content": [ @@ -230,7 +230,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -246,7 +246,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -255,7 +255,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:53:26.068740315" + "timestamp": "2026-02-06T14:16:59.025003686" }, "homo_sapiens - illumina - cram, crai, fasta, fai, []": { "content": [ @@ -266,14 +266,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,6d536dae721eb082f0ba0216f67a340f" + "test.tsv.gz:md5,f5f1035e4296fd299dc47947fa0b4c01" ] ], "1": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -282,14 +282,14 @@ "id": "test", "single_end": false }, - "test.tsv.gz:md5,6d536dae721eb082f0ba0216f67a340f" + "test.tsv.gz:md5,f5f1035e4296fd299dc47947fa0b4c01" ] ], "versions_perbase": [ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -298,7 +298,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:51:43.208109165" + "timestamp": "2026-02-06T14:15:17.938018267" }, "homo_sapiens - illumina - cram, crai, fasta, fai, bed - stub": { "content": [ @@ -316,7 +316,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ], "tsv": [ @@ -332,7 +332,7 @@ [ "PERBASE", "perbase", - "1.2.0" + "1.4.0" ] ] } @@ -341,6 +341,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-01-28T16:52:52.730988602" + "timestamp": "2026-02-06T14:16:25.613409317" } } \ No newline at end of file From 1616bd17361f70368c75902c186a7b04b158ac1b Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Thu, 19 Feb 2026 13:48:51 +0000 Subject: [PATCH 6/6] rm versions.yml from meta.yml --- modules/nf-core/perbase/meta.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/modules/nf-core/perbase/meta.yml b/modules/nf-core/perbase/meta.yml index 523f59b3c0e5..5eeb68543319 100644 --- a/modules/nf-core/perbase/meta.yml +++ b/modules/nf-core/perbase/meta.yml @@ -71,14 +71,6 @@ output: ontologies: - edam: "http://edamontology.org/format_3475" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML versions_perbase: - - ${task.process}: type: string