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Merged
SPPearce merged 12 commits into from
Dec 23, 2025
Merged

Ngscheckmate topics #9597

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0154d02
Start of topics conversion
SPPearce Dec 21, 2025
7b5cf32
Swap ngscheckmate to topic
SPPearce Dec 21, 2025
f0cc5fd
Remove trailing whitespace
SPPearce Dec 21, 2025
f8eefde
Update snapshots
SPPearce Dec 21, 2025
31b5d63
Update test
SPPearce Dec 21, 2025
ed149b3
Update snapshots
SPPearce Dec 22, 2025
4290656
Merge remote-tracking branch 'origin/master' into ngscheckmate_topics
SPPearce Dec 22, 2025
4a28dd7
Skip two submodules on conda
SPPearce Dec 22, 2025
adcd88b
Address comments
SPPearce Dec 23, 2025
ce27de7
Update snapshot
SPPearce Dec 23, 2025
52cd404
Merge branch 'master' into ngscheckmate_topics
LouisLeNezet Dec 23, 2025
07a0d39
Update snapshot
SPPearce Dec 23, 2025
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2 changes: 2 additions & 0 deletions .github/skip_nf_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,8 @@
"modules/nf-core/mitohifi/mitohifi",
"modules/nf-core/molkartgarage/clahe",
"modules/nf-core/ncbitools/vecscreen",
"modules/nf-core/ngscheckmate/fastq",
"modules/nf-core/ngscheckmate/vafncm",
Comment on lines +75 to +76
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@maxulysse maxulysse Jan 7, 2026

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why?

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@SPPearce SPPearce Jan 7, 2026

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They were crashing on conda

"modules/nf-core/parabricks",
"modules/nf-core/purgedups/calcuts",
"modules/nf-core/purgedups/getseqs",
Expand Down
15 changes: 2 additions & 13 deletions modules/nf-core/ngscheckmate/fastq/main.nf
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Expand Up @@ -13,7 +13,7 @@ process NGSCHECKMATE_FASTQ {

output:
tuple val(meta), path("*.vaf"), emit: vaf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate

when:
task.ext.when == null || task.ext.when
Expand All @@ -24,23 +24,12 @@ process NGSCHECKMATE_FASTQ {
def fastq2command = ( reads instanceof List && reads.size() == 2 ) ? " -2 ${reads[1]} " : ""

"""
ngscheckmate_fastq -1 ${reads[0]} $fastq2command ${snp_pt} -p ${task.cpus} $args > ${prefix}.vaf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
END_VERSIONS
ngscheckmate_fastq -1 ${reads[0]} $fastq2command ${snp_pt} -p ${task.cpus} $args > ${prefix}.vaf
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vaf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
END_VERSIONS
"""
}
27 changes: 21 additions & 6 deletions modules/nf-core/ngscheckmate/fastq/meta.yml
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Expand Up @@ -55,13 +55,28 @@ output:
position contained in the PT file.
pattern: "*.{vaf}"
ontologies: []
versions_ngscheckmate:
- - ${task.process}:
type: string
description: The process the versions were collected from
- ngscheckmate:
type: string
description: The tool name
- "ncm.py --help | sed '7!d;s/.* v//g'":
type: string
description: The command used to generate 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 process the versions were collected from
- ngscheckmate:
type: string
description: The tool name
- "ncm.py --help | sed '7!d;s/.* v//g'":
type: string
description: The command used to generate the version of the tool
authors:
- "@sppearce"
maintainers:
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/ngscheckmate/fastq/tests/main.nf.test
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Expand Up @@ -96,8 +96,8 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
Expand All @@ -124,9 +124,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

Expand Down
40 changes: 28 additions & 12 deletions modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap
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Expand Up @@ -12,7 +12,11 @@
]
],
"1": [
"versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
[
"NGSCHECKMATE_FASTQ",
"ngscheckmate",
"1.0.1"
]
],
"vaf": [
[
Expand All @@ -23,16 +27,20 @@
"test_paired.vaf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
"versions_ngscheckmate": [
[
"NGSCHECKMATE_FASTQ",
"ngscheckmate",
"1.0.1"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2024-06-18T09:05:52.332885973"
"timestamp": "2025-12-22T08:42:48.87004401"
},
"sarscov2 - bam": {
"content": [
Expand All @@ -47,7 +55,11 @@
]
],
"1": [
"versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
[
"NGSCHECKMATE_FASTQ",
"ngscheckmate",
"1.0.1"
]
],
"vaf": [
[
Expand All @@ -58,15 +70,19 @@
"test_paired.vaf:md5,a2d18480c8bb7045c39c063faef7e1e4"
]
],
"versions": [
"versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
"versions_ngscheckmate": [
[
"NGSCHECKMATE_FASTQ",
"ngscheckmate",
"1.0.1"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2024-06-18T09:10:36.450684266"
"timestamp": "2025-12-23T09:03:49.545360371"
}
}
14 changes: 2 additions & 12 deletions modules/nf-core/ngscheckmate/ncm/main.nf
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Expand Up @@ -17,15 +17,15 @@ process NGSCHECKMATE_NCM {
tuple val(meta), path("*_all.txt"), emit: all
tuple val(meta), path("*.pdf"), emit: pdf, optional: true
tuple val(meta), path("*.vcf"), emit: vcf, optional: true
path "versions.yml", emit: versions
tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def unzip = files.any { it.toString().endsWith(".vcf.gz") }
def unzip = files.any {file -> file.toString().endsWith(".vcf.gz") }
"""
if ${unzip}
then
Expand All @@ -40,11 +40,6 @@ process NGSCHECKMATE_NCM {
then
rm -f *.vcf # clean up decompressed vcfs
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
END_VERSIONS
"""

stub:
Expand All @@ -54,10 +49,5 @@ process NGSCHECKMATE_NCM {
touch ${prefix}_matched.txt
touch ${prefix}_all.txt
touch ${prefix}.pdf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
END_VERSIONS
"""
}
27 changes: 21 additions & 6 deletions modules/nf-core/ngscheckmate/ncm/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -106,13 +106,28 @@ output:
calls used
pattern: "*.vcf"
ontologies: []
versions_ngscheckmate:
- - ${task.process}:
type: string
description: The process the versions were collected from
- ngscheckmate:
type: string
description: The tool name
- "ncm.py --help | sed '7!d;s/.* v//g'":
type: string
description: The command used to generate 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 process the versions were collected from
- ngscheckmate:
type: string
description: The tool name
- "ncm.py --help | sed '7!d;s/.* v//g'":
type: string
description: The command used to generate the version of the tool
authors:
- "@sppearce"
maintainers:
Expand Down
29 changes: 16 additions & 13 deletions modules/nf-core/ngscheckmate/ncm/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -75,14 +75,15 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.corr_matrix[0][1]).name, // Content md5 not stable under conda
file(process.out.matched[0][1]).name, // Content md5 not stable under conda
file(process.out.all[0][1]).name, // Content md5 not stable under conda
process.out.versions
).match() }
file(process.out.corr_matrix[0][1]).name,
file(process.out.matched[0][1]).name,
file(process.out.all[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
}

Expand All @@ -106,15 +107,16 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.corr_matrix,
file(process.out.matched[0][1]).name,
process.out.all,
file(process.out.pdf[0][1]).name,
process.out.versions
).match() }
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
}

Expand Down Expand Up @@ -144,9 +146,10 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()
}
)
}

Expand All @@ -169,9 +172,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

Expand Down
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