From ae9e068dd808bb5d08285ac251039e4537948f82 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Thu, 22 Jan 2026 14:17:43 +0000 Subject: [PATCH 1/4] migrate untar to versions topic --- modules/nf-core/untar/main.nf | 12 +-- modules/nf-core/untar/meta.yml | 28 +++++-- modules/nf-core/untar/tests/main.nf.test.snap | 80 +++++++++++++------ 3 files changed, 79 insertions(+), 41 deletions(-) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index e712ebe63ab5..fa4642583a63 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -12,7 +12,7 @@ process UNTAR { output: tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions + tuple val("${task.process}"), val('tar'), eval("tar --version | head -n 1 | cut -f4 -d ' '"), topic: versions, emit: versions_tar when: task.ext.when == null || task.ext.when @@ -42,11 +42,6 @@ process UNTAR { ${archive} \\ ${args2} fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ stub: @@ -75,10 +70,5 @@ process UNTAR { fi done fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index 1603e3829658..db20b1ec0d05 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -38,18 +38,34 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*/" + versions_tar: + - - ${task.process}: + type: string + description: The name of the process + - tar: + type: string + description: The name of the tool + - "tar --version | head -n 1 | cut -f4 -d ' '": + 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 + - tar: + type: string + description: The name of the tool + - "tar --version | head -n 1 | cut -f4 -d ' '": + type: eval + description: The expression to obtain the version of the tool authors: - "@joseespinosa" - "@drpatelh" - "@matthdsm" - "@jfy133" + - "@eit-maxlcummins" maintainers: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index ceb91b7925ca..52b0e728eab8 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -13,7 +13,11 @@ ] ], "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + [ + "UNTAR", + "tar", + "1.34" + ] ], "untar": [ [ @@ -25,16 +29,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + "versions_tar": [ + [ + "UNTAR", + "tar", + "1.34" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:28.231047" + "timestamp": "2026-01-22T14:15:23.063536907" }, "test_untar_onlyfiles - stub": { "content": [ @@ -50,7 +58,11 @@ ] ], "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + [ + "UNTAR", + "tar", + "1.34" + ] ], "untar": [ [ @@ -62,16 +74,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + "versions_tar": [ + [ + "UNTAR", + "tar", + "1.34" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:45.773103" + "timestamp": "2026-01-22T14:15:34.84221815" }, "test_untar - stub": { "content": [ @@ -89,7 +105,11 @@ ] ], "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + [ + "UNTAR", + "tar", + "1.34" + ] ], "untar": [ [ @@ -103,16 +123,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + "versions_tar": [ + [ + "UNTAR", + "tar", + "1.34" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:36.777441" + "timestamp": "2026-01-22T14:15:28.946517024" }, "test_untar": { "content": [ @@ -130,7 +154,11 @@ ] ], "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + [ + "UNTAR", + "tar", + "1.34" + ] ], "untar": [ [ @@ -144,15 +172,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + "versions_tar": [ + [ + "UNTAR", + "tar", + "1.34" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:19.377674" + "timestamp": "2026-01-22T14:15:17.05337819" } } \ No newline at end of file From 3d1ff45cc4f43b0a9533a7df120f9bcf52a4cc9b Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 30 Jan 2026 14:57:39 +0000 Subject: [PATCH 2/4] remove version capture from subworkflow featuring tar --- subworkflows/nf-core/fasta_index_methylseq/main.nf | 3 --- 1 file changed, 3 deletions(-) diff --git a/subworkflows/nf-core/fasta_index_methylseq/main.nf b/subworkflows/nf-core/fasta_index_methylseq/main.nf index 81f9f1562967..7fe7c205acc0 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/main.nf +++ b/subworkflows/nf-core/fasta_index_methylseq/main.nf @@ -61,7 +61,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) - ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { if( aligner == "bismark_hisat") { @@ -99,7 +98,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR_BWAMETH.out.untar) - ch_versions = ch_versions.mix(UNTAR_BWAMETH.out.versions) } else { BWAMETH_INDEX ( ch_fasta, @@ -129,7 +127,6 @@ workflow FASTA_INDEX_METHYLSEQ { ) ch_bwamem_index = ch_bwamem_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) - ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { log.info "BWA index not provided. Generating BWA index from FASTA file." BWA_INDEX ( From 4f2653a83b8e2604bd4df72da722ceab1154507a Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 30 Jan 2026 15:03:47 +0000 Subject: [PATCH 3/4] update snapshot for subworkflow using untar --- .../tests/main.nf.test.snap | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap index 33405685d70d..937022f214d4 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap @@ -88,14 +88,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:26.091313" + "timestamp": "2026-01-30T14:59:55.522877681" }, "Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": { "content": [ @@ -138,14 +138,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:07.137329" + "timestamp": "2026-01-30T15:00:41.155544826" }, "Params: bwameth | generate fasta index | generate bwameth mem2 index": { "content": [ @@ -246,14 +246,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:41:32.513035" + "timestamp": "2026-01-30T14:58:55.776272926" }, "Params: bwameth | generate fasta index | download bwameth mem2 index | collecthsmetrics": { "content": [ @@ -295,14 +295,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:43:14.983559" + "timestamp": "2026-01-30T15:00:48.278308395" }, "Params: bwameth | generate fasta index | download bwameth mem2 index": { "content": [ @@ -344,14 +344,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:33.433615" + "timestamp": "2026-01-30T15:00:03.137422619" }, "Params: bwameth | generate fasta index | generate bwameth index": { "content": [ @@ -456,14 +456,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:03.741859" + "timestamp": "2026-01-30T14:59:33.136861469" }, "Params: bismark_hisat | download bismark index (hisat2)": { "content": [ @@ -519,14 +519,14 @@ ], [ - "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:41:55.807647" + "timestamp": "2026-01-30T14:59:26.335141572" }, "Params: bwameth | download fasta index | download bwameth index": { "content": [ @@ -569,14 +569,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:10.926869" + "timestamp": "2026-01-30T14:59:40.761686505" }, "Params: bwameth | download fasta index | download bwameth mem2 index": { "content": [ @@ -618,14 +618,14 @@ ], [ - "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-19T15:42:18.694983" + "timestamp": "2026-01-30T14:59:48.088868576" }, "Params: bwamem | generate fasta index | generate bwamem index": { "content": [ From 9dccfcbba8401a2b767bc20ed6e54531a92bb815 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 30 Jan 2026 15:06:15 +0000 Subject: [PATCH 4/4] add check for versions in tests for untar --- modules/nf-core/untar/tests/main.nf.test | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index c957517aaa6b..ca5492fcbd6c 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -20,7 +20,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -38,7 +40,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -58,7 +62,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -78,7 +84,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } }