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Update whamg: topic versions, stub block, sanitizeOutput #11450

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Update whamg: topic versions, stub block, sanitizeOutput #11450

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5994a77
feat(whamg): migrate to topic: versions, add stub block, sanitizeOutp…
HReed1 Apr 30, 2026
c489f4f
Standardize version emission and restore EDAM comments
HReed1 May 1, 2026
a539828
fix(whamg): rename emit to versions_whamg per nf-core convention
HReed1 May 1, 2026
b559aa1
Merge branch 'master' into stub-topics-whamg
HReed1 May 3, 2026
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14 changes: 9 additions & 5 deletions modules/nf-core/whamg/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process WHAMG {
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi
tuple val(meta), path("*.txt") , emit: graph, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('whamg'), eval('whamg 2>&1 | grep Version | sed \'s/^Version: v//; s/-.*$//\''), topic: versions, emit: versions_whamg

when:
task.ext.when == null || task.ext.when
Expand All @@ -36,10 +36,14 @@ process WHAMG {
| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz

tabix ${args3} ${prefix}.vcf.gz
"""

cat <<-END_VERSIONS > versions.yml
"${task.process}":
whamg: \$(echo \$(whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*\$//' ))
END_VERSIONS
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
echo "" | gzip > ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
"""
}
36 changes: 26 additions & 10 deletions modules/nf-core/whamg/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
name: "whamg"
description: The wham suite consists of two programs, wham and whamg. wham, the original
tool, is a very sensitive method with a high false discovery rate. The second program,
whamg, is more accurate and better suited for general structural variant (SV) discovery.
description: The wham suite consists of two programs, wham and whamg. wham, the
original tool, is a very sensitive method with a high false discovery rate.
The second program, whamg, is more accurate and better suited for general
structural variant (SV) discovery.
keywords:
- whamg
- wham
Expand All @@ -15,7 +16,8 @@ tools:
documentation: "https://github.com/zeeev/wham"
tool_dev_url: "https://github.com/zeeev/wham"
doi: "10.1371/journal.pcbi.1004572"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -78,13 +80,27 @@ output:
description: Graph file
pattern: "*.txt"
ontologies: []
versions_whamg:
- - ${task.process}:
type: string
description: The name of the process
- whamg:
type: string
description: The name of the tool
- "whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*$//'":
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
- - ${task.process}:
type: string
description: The name of the process
- whamg:
type: string
description: The name of the tool
- "whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*$//'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@nvnieuwk"
maintainers:
Expand Down
35 changes: 28 additions & 7 deletions modules/nf-core/whamg/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,34 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
path(process.out.vcf[0][1]).vcf.summary,
file(process.out.tbi[0][1]).name,
Comment on lines -34 to -35
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@SPPearce SPPearce May 1, 2026

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vcf and tbi files are typically unstable due to differences between conda/docker/singularity.
The vcf summary command comes from the nft-vcf plugin.
Any time you see a snapshot split out like this it means you need to take special care and not just snapshot the whole process.out.
You can use unstableKeys for the tbi channel, but the vcf summary is useful to keep for showing the vcf file is not changing.

process.out.graph,
process.out.versions
).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match() }
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@SPPearce SPPearce May 4, 2026

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Still need to swap back to use nft-vcf for the vcf file, and the tbi is unstable

)
}
}

test("test-whamg-bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
81 changes: 69 additions & 12 deletions modules/nf-core/whamg/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,19 +1,76 @@
{
"test-whamg-bam": {
"content": [
"VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]",
"test.vcf.gz.tbi",
[

],
[
"versions.yml:md5,243bed402cdc21ab2fc42a7400399ea9"
]
{
"graph": [

],
"tbi": [
[
{
"id": "test"
},
"test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,e45326a91ef59ea91ad3fe85f353748c"
]
],
"versions_whamg": [
[
"WHAMG",
"whamg",
"1.7.0"
]
]
}
],
"timestamp": "2026-04-30T17:44:50.968503",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-27T11:43:16.953021"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"test-whamg-bam - stub": {
"content": [
{
"graph": [

],
"tbi": [
[
{
"id": "test"
},
"test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions_whamg": [
[
"WHAMG",
"whamg",
"1.7.0"
]
]
}
],
"timestamp": "2026-04-30T17:44:56.533951",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
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