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Merged
SPPearce merged 4 commits into from
Aug 3, 2026
+118 −89
Merged

Migrate vcf2maf versions topic #12477

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371ca44
chore: migrate vcf2maf versions topic
atrigila Jul 31, 2026
18de73a
Merge branch 'master' into migrate-topics-vcf2maf
atrigila Jul 31, 2026
c27f460
style: fix linting
atrigila Jul 31, 2026
3d0d0a9
Merge branch 'migrate-topics-vcf2maf' of https://github.com/atrigila/…
atrigila Jul 31, 2026
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13 changes: 2 additions & 11 deletions modules/nf-core/vcf2maf/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ process VCF2MAF {

output:
tuple val(meta), path("*.maf"), emit: maf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('vcf2maf'), val("1.6.22"), emit: versions_vcf2maf, topic: versions
tuple val("${task.process}"), val('ensemblvep'), eval('vep --help 2>&1 | sed -n "s/^ ensembl-vep *: //p"'), emit: versions_ensemblvep, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -42,11 +43,6 @@ process VCF2MAF {
--ref-fasta $fasta \\
--input-vcf $vcf \\
--output-maf ${prefix}.maf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcf2maf: $VERSION\$VEP_VERSION
END_VERSIONS
"""

stub:
Expand All @@ -60,10 +56,5 @@ process VCF2MAF {
fi

touch ${prefix}.maf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcf2maf: $VERSION\$VEP_VERSION
END_VERSIONS
"""
}
45 changes: 39 additions & 6 deletions modules/nf-core/vcf2maf/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,46 @@ output:
description: MAF file produced from VCF
pattern: "*.maf"
ontologies: []
versions_vcf2maf:
- - ${task.process}:
type: string
description: The name of the process
- vcf2maf:
type: string
description: The name of the tool
- "1.6.22":
type: string
description: The expression to obtain the version of the tool
versions_ensemblvep:
- - ${task.process}:
type: string
description: The name of the process
- ensemblvep:
type: string
description: The name of the tool
- 'vep --help 2>&1 | sed -n "s/^ ensembl-vep *: //p"':
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
- vcf2maf:
type: string
description: The name of the tool
- "1.6.22":
type: string
description: The expression to obtain the version of the tool
- - ${task.process}:
type: string
description: The name of the process
- ensemblvep:
type: string
description: The name of the tool
- 'vep --help 2>&1 | sed -n "s/^ ensembl-vep *: //p"':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@adamrtalbot"
maintainers:
Expand Down
11 changes: 4 additions & 7 deletions modules/nf-core/vcf2maf/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
path(process.out.maf[0][1]).readLines()[5..131],
process.out.versions,
path(process.out.versions[0]).readLines()
process.out.findAll { key, val -> key.startsWith('versions') }
).match() },
)
}
Expand Down Expand Up @@ -78,7 +77,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines
{ assert snapshot(process.out.versions, path(process.out.versions[0]).readLines()).match() }
{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
)
}
}
Expand All @@ -103,8 +102,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).readLines()
sanitizeOutput(process.out)
).match()
},
)
Expand Down Expand Up @@ -132,8 +130,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).readLines()
sanitizeOutput(process.out)
).match()
},
)
Expand Down
138 changes: 73 additions & 65 deletions modules/nf-core/vcf2maf/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,94 +2,93 @@
"Run with VEP - stub": {
"content": [
{
"0": [
"maf": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
],
"maf": [
"versions_ensemblvep": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
"VCF2MAF",
"ensemblvep",
"113.0"
]
],
"versions": [
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
"versions_vcf2maf": [
[
"VCF2MAF",
"vcf2maf",
"1.6.22"
]
]
},
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22",
" ensemblvep: 113.0"
]
}
],
"timestamp": "2026-07-31T16:35:17.149691833",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T16:01:35.707312"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"Run with VEP": {
"content": [
[
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
],
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22",
" ensemblvep: 113.0"
]
{
"versions_ensemblvep": [
[
"VCF2MAF",
"ensemblvep",
"113.0"
]
],
"versions_vcf2maf": [
[
"VCF2MAF",
"vcf2maf",
"1.6.22"
]
]
}
],
"timestamp": "2026-07-31T15:38:16.241168051",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-12-11T15:50:59.184221"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"Run without VEP - stub": {
"content": [
{
"0": [
"maf": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
],
"maf": [
"versions_ensemblvep": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
"VCF2MAF",
"ensemblvep",
"113.0"
]
],
"versions": [
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
"versions_vcf2maf": [
[
"VCF2MAF",
"vcf2maf",
"1.6.22"
]
]
},
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22"
]
}
],
"timestamp": "2026-07-31T16:35:08.154659422",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:49:39.498519"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"Run without VEP": {
"content": [
Expand Down Expand Up @@ -222,18 +221,27 @@
"Unknown\t0\t.\tGRCh38\tchr22\t4606\t4606\t+\tTargeted_Region\tINS\tT\tT\t<NON_REF>\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTC\t.\t.\t\t\t\t\t\t\t\t\t\t4606",
"Unknown\t0\t.\tGRCh38\tchr22\t4608\t4608\t+\tTargeted_Region\tINS\tA\tA\t<NON_REF>\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAA\t.\t.\t\t\t\t\t\t\t\t\t\t4608"
],
[
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
],
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22"
]
{
"versions_ensemblvep": [
[
"VCF2MAF",
"ensemblvep",
"113.0"
]
],
"versions_vcf2maf": [
[
"VCF2MAF",
"vcf2maf",
"1.6.22"
]
]
}
],
"timestamp": "2026-07-31T15:38:06.822105654",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:52:16.957598"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
}