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Merged
camlloyd merged 11 commits into from
Mar 16, 2026
Merged

update module: duphold #10822

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7353a2a
Update main.nf
camlloyd Mar 13, 2026
c7c8ccb
Update meta.yml
camlloyd Mar 13, 2026
80f331f
Update main.nf.test
camlloyd Mar 13, 2026
7b806d4
Update snaps
camlloyd Mar 13, 2026
2661dbf
Add bio.tools ID
camlloyd Mar 13, 2026
12cf6ea
Update modules/nf-core/duphold/main.nf
camlloyd Mar 13, 2026
1a873ea
Update meta.yml
camlloyd Mar 13, 2026
ebe2365
Fix version
camlloyd Mar 16, 2026
ba5c04d
Update meta.yml
camlloyd Mar 16, 2026
a650c7a
Merge branch 'master' into duphold
camlloyd Mar 16, 2026
c741c5d
Update meta.yml
camlloyd Mar 16, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/duphold/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process DUPHOLD {

output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('duphold'), eval('duphold -h | sed -e "s/^version: //;q"'), emit: versions_duphold, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -34,21 +34,11 @@ process DUPHOLD {
--bam ${alignment_file} \\
--fasta ${fasta} \\
${snp_annotation}


cat <<-END_VERSIONS > versions.yml
"${task.process}":
duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
END_VERSIONS
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
END_VERSIONS
"""
}
31 changes: 23 additions & 8 deletions modules/nf-core/duphold/meta.yml
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Expand Up @@ -18,8 +18,9 @@ tools:
documentation: "https://github.com/brentp/duphold"
tool_dev_url: "https://github.com/brentp/duphold"
doi: "10.1093/gigascience/giz040"
licence: ["MIT"]
identifier: ""
licence:
- "MIT"
identifier: biotools:duphold
input:
- - meta:
type: map
Expand Down Expand Up @@ -71,13 +72,27 @@ output:
pattern: "*.vcf.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
versions_duphold:
- - ${task.process}:
type: string
description: The name of the process
- duphold:
type: string
description: The name of the tool
- 'duphold -h | sed -e "s/^version: //;q"':
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
- duphold:
type: string
description: The name of the tool
- 'duphold -h | sed -e "s/^version: //;q"':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@nvnieuwk"
maintainers:
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/duphold/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { key, val -> key.startsWith('versions') },
process.out.vcf.collect{ [
path(it[1]).vcf.summary,
path(it[1]).vcf.variantsMD5
Expand Down Expand Up @@ -63,7 +63,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { key, val -> key.startsWith('versions') },
process.out.vcf.collect{ [
path(it[1]).vcf.summary,
path(it[1]).vcf.variantsMD5
Expand Down Expand Up @@ -94,7 +94,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { key, val -> key.startsWith('versions') },
process.out.vcf.collect{ [
path(it[1]).vcf.summary,
path(it[1]).vcf.variantsMD5
Expand Down
88 changes: 55 additions & 33 deletions modules/nf-core/duphold/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,57 +1,75 @@
{
"homo_sapiens - bam gvcf - fasta": {
"content": [
[
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
],
{
"versions_duphold": [
[
"DUPHOLD",
"duphold",
"0.2.1"
]
]
},
[
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
"a65760baa4ccf726b1d30f590d88bc81"
]
]
],
"timestamp": "2026-03-13T11:07:13.139440214",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-26T12:29:08.458156285"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"homo_sapiens - bam gvcf snp - fasta": {
"content": [
[
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
],
{
"versions_duphold": [
[
"DUPHOLD",
"duphold",
"0.2.1"
]
]
},
[
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
"a65760baa4ccf726b1d30f590d88bc81"
]
]
],
"timestamp": "2026-03-13T11:10:11.886968148",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-26T12:29:24.054557879"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"homo_sapiens - cram gvcf - fasta": {
"content": [
[
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
],
{
"versions_duphold": [
[
"DUPHOLD",
"duphold",
"0.2.1"
]
]
},
[
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
"a65760baa4ccf726b1d30f590d88bc81"
]
]
],
"timestamp": "2026-03-13T11:07:20.967522367",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-26T12:29:16.114897779"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"homo_sapiens - bam gvcf - fasta -- stub": {
"content": [
Expand All @@ -65,7 +83,11 @@
]
],
"1": [
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
[
"DUPHOLD",
"duphold",
"0.2.1"
]
],
"vcf": [
[
Expand All @@ -75,22 +97,22 @@
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
"versions_duphold": [
[
"DUPHOLD",
"duphold",
"0.2.1"
]
]
},
[
{
"DUPHOLD": {
"duphold": "0.2.1"
}
}

]
],
"timestamp": "2026-03-13T11:04:28.096812722",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-26T09:46:42.503938847"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
}
}
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