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update module: duphold (nf-core#10822)
* Update main.nf * Update meta.yml * Update main.nf.test * Update snaps * Add bio.tools ID * Update modules/nf-core/duphold/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Update meta.yml * Fix version * Update meta.yml * Update meta.yml --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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+82
-55
lines changed

4 files changed

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lines changed

‎modules/nf-core/duphold/main.nf‎

Lines changed: 1 addition & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ process DUPHOLD {
1414

1515
output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
17-
path "versions.yml" , emit: versions
17+
tuple val("${task.process}"), val('duphold'), eval('duphold -h | sed -e "s/^version: //;q"'), emit: versions_duphold, topic: versions
1818

1919
when:
2020
task.ext.when == null || task.ext.when
@@ -34,21 +34,11 @@ process DUPHOLD {
3434
--bam ${alignment_file} \\
3535
--fasta ${fasta} \\
3636
${snp_annotation}
37-
38-
39-
cat <<-END_VERSIONS > versions.yml
40-
"${task.process}":
41-
duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
42-
END_VERSIONS
4337
"""
4438

4539
stub:
4640
prefix = task.ext.prefix ?: "${meta.id}"
4741
"""
4842
echo "" | gzip > ${prefix}.vcf.gz
49-
cat <<-END_VERSIONS > versions.yml
50-
"${task.process}":
51-
duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
52-
END_VERSIONS
5343
"""
5444
}

‎modules/nf-core/duphold/meta.yml‎

Lines changed: 23 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -18,8 +18,9 @@ tools:
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documentation: "https://github.com/brentp/duphold"
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tool_dev_url: "https://github.com/brentp/duphold"
2020
doi: "10.1093/gigascience/giz040"
21-
licence: ["MIT"]
22-
identifier: ""
21+
licence:
22+
- "MIT"
23+
identifier: biotools:duphold
2324
input:
2425
- - meta:
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type: map
@@ -71,13 +72,27 @@ output:
7172
pattern: "*.vcf.gz"
7273
ontologies:
7374
- edam: http://edamontology.org/format_3989 # GZIP format
75+
versions_duphold:
76+
- - ${task.process}:
77+
type: string
78+
description: The name of the process
79+
- duphold:
80+
type: string
81+
description: The name of the tool
82+
- 'duphold -h | sed -e "s/^version: //;q"':
83+
type: eval
84+
description: The expression to obtain the version of the tool
85+
topics:
7486
versions:
75-
- versions.yml:
76-
type: file
77-
description: File containing software versions
78-
pattern: "versions.yml"
79-
ontologies:
80-
- edam: http://edamontology.org/format_3750 # YAML
87+
- - ${task.process}:
88+
type: string
89+
description: The name of the process
90+
- duphold:
91+
type: string
92+
description: The name of the tool
93+
- 'duphold -h | sed -e "s/^version: //;q"':
94+
type: eval
95+
description: The expression to obtain the version of the tool
8196
authors:
8297
- "@nvnieuwk"
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maintainers:

‎modules/nf-core/duphold/tests/main.nf.test‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ nextflow_process {
3030
assertAll(
3131
{ assert process.success },
3232
{ assert snapshot(
33-
process.out.versions,
33+
process.out.findAll { key, val -> key.startsWith('versions') },
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process.out.vcf.collect{ [
3535
path(it[1]).vcf.summary,
3636
path(it[1]).vcf.variantsMD5
@@ -63,7 +63,7 @@ nextflow_process {
6363
assertAll(
6464
{ assert process.success },
6565
{ assert snapshot(
66-
process.out.versions,
66+
process.out.findAll { key, val -> key.startsWith('versions') },
6767
process.out.vcf.collect{ [
6868
path(it[1]).vcf.summary,
6969
path(it[1]).vcf.variantsMD5
@@ -94,7 +94,7 @@ nextflow_process {
9494
assertAll(
9595
{ assert process.success },
9696
{ assert snapshot(
97-
process.out.versions,
97+
process.out.findAll { key, val -> key.startsWith('versions') },
9898
process.out.vcf.collect{ [
9999
path(it[1]).vcf.summary,
100100
path(it[1]).vcf.variantsMD5

‎modules/nf-core/duphold/tests/main.nf.test.snap‎

Lines changed: 55 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,57 +1,75 @@
11
{
22
"homo_sapiens - bam gvcf - fasta": {
33
"content": [
4-
[
5-
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
6-
],
4+
{
5+
"versions_duphold": [
6+
[
7+
"DUPHOLD",
8+
"duphold",
9+
"0.2.1"
10+
]
11+
]
12+
},
713
[
814
[
915
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
1016
"a65760baa4ccf726b1d30f590d88bc81"
1117
]
1218
]
1319
],
20+
"timestamp": "2026-03-13T11:07:13.139440214",
1421
"meta": {
15-
"nf-test": "0.9.2",
16-
"nextflow": "24.10.5"
17-
},
18-
"timestamp": "2025-03-26T12:29:08.458156285"
22+
"nf-test": "0.9.4",
23+
"nextflow": "25.10.4"
24+
}
1925
},
2026
"homo_sapiens - bam gvcf snp - fasta": {
2127
"content": [
22-
[
23-
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
24-
],
28+
{
29+
"versions_duphold": [
30+
[
31+
"DUPHOLD",
32+
"duphold",
33+
"0.2.1"
34+
]
35+
]
36+
},
2537
[
2638
[
2739
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
2840
"a65760baa4ccf726b1d30f590d88bc81"
2941
]
3042
]
3143
],
44+
"timestamp": "2026-03-13T11:10:11.886968148",
3245
"meta": {
33-
"nf-test": "0.9.2",
34-
"nextflow": "24.10.5"
35-
},
36-
"timestamp": "2025-03-26T12:29:24.054557879"
46+
"nf-test": "0.9.4",
47+
"nextflow": "25.10.4"
48+
}
3749
},
3850
"homo_sapiens - cram gvcf - fasta": {
3951
"content": [
40-
[
41-
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
42-
],
52+
{
53+
"versions_duphold": [
54+
[
55+
"DUPHOLD",
56+
"duphold",
57+
"0.2.1"
58+
]
59+
]
60+
},
4361
[
4462
[
4563
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
4664
"a65760baa4ccf726b1d30f590d88bc81"
4765
]
4866
]
4967
],
68+
"timestamp": "2026-03-13T11:07:20.967522367",
5069
"meta": {
51-
"nf-test": "0.9.2",
52-
"nextflow": "24.10.5"
53-
},
54-
"timestamp": "2025-03-26T12:29:16.114897779"
70+
"nf-test": "0.9.4",
71+
"nextflow": "25.10.4"
72+
}
5573
},
5674
"homo_sapiens - bam gvcf - fasta -- stub": {
5775
"content": [
@@ -65,7 +83,11 @@
6583
]
6684
],
6785
"1": [
68-
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
86+
[
87+
"DUPHOLD",
88+
"duphold",
89+
"0.2.1"
90+
]
6991
],
7092
"vcf": [
7193
[
@@ -75,22 +97,22 @@
7597
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
7698
]
7799
],
78-
"versions": [
79-
"versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
100+
"versions_duphold": [
101+
[
102+
"DUPHOLD",
103+
"duphold",
104+
"0.2.1"
105+
]
80106
]
81107
},
82108
[
83-
{
84-
"DUPHOLD": {
85-
"duphold": "0.2.1"
86-
}
87-
}
109+
88110
]
89111
],
112+
"timestamp": "2026-03-13T11:04:28.096812722",
90113
"meta": {
91-
"nf-test": "0.9.2",
92-
"nextflow": "24.10.5"
93-
},
94-
"timestamp": "2025-03-26T09:46:42.503938847"
114+
"nf-test": "0.9.4",
115+
"nextflow": "25.10.4"
116+
}
95117
}
96118
}

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