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Merged
fellen31 merged 2 commits into from
Dec 22, 2025
Merged

Bump genmod to 3.10.2 and switch to topics #9603

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6691b42
Bump genmod to 3.10.2 and switch to topics
fellen31 Dec 22, 2025
31efaf6
Add md5sum for stable subcommands
fellen31 Dec 22, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/genmod/annotate/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::genmod=3.10.1
- bioconda::genmod=3.10.2
16 changes: 3 additions & 13 deletions modules/nf-core/genmod/annotate/main.nf
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Expand Up @@ -4,15 +4,15 @@ process GENMOD_ANNOTATE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"

input:
tuple val(meta), path(input_vcf)

output:
tuple val(meta), path("*_annotate.vcf"), emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -26,21 +26,11 @@ process GENMOD_ANNOTATE {
$args \\
--outfile ${prefix}_annotate.vcf \\
$input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_annotate.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/genmod/annotate/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,27 @@ output:
description: Annotated VCF file
pattern: "*.{vcf}"
ontologies: []
versions_genmod:
- - ${task.process}:
type: string
description: Name of the process
- genmod:
type: string
description: Name of the tool
- "genmod --version | sed 's/^.*genmod version: //'":
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: Name of the process
- genmod:
type: string
description: Name of the tool
- "genmod --version | sed 's/^.*genmod version: //'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@ramprasadn"
maintainers:
Expand Down
5 changes: 3 additions & 2 deletions modules/nf-core/genmod/annotate/tests/main.nf.test
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Expand Up @@ -26,9 +26,10 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.vcf.get(0).get(1)).vcf.summary,
).match() }
path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
process.out.findAll { key, val -> key.startsWith("versions") },
).match() }
)
}

Expand Down
41 changes: 28 additions & 13 deletions modules/nf-core/genmod/annotate/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,16 +1,23 @@
{
"genmod_annotate": {
"content": [
[
"versions.yml:md5,06246c96ae9b676262e12828d29a388b"
],
"VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
"VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]",
"ec9b1d7d21c9f6c0a6e0dffb56732fc3",
{
"versions_genmod": [
[
"GENMOD_ANNOTATE",
"genmod",
"3.10.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2025-04-16T11:25:17.894083851"
"timestamp": "2025-12-22T14:45:39.879885252"
},
"genmod_annotate - stub": {
"content": [
Expand All @@ -25,7 +32,11 @@
]
],
"1": [
"versions.yml:md5,06246c96ae9b676262e12828d29a388b"
[
"GENMOD_ANNOTATE",
"genmod",
"3.10.2"
]
],
"vcf": [
[
Expand All @@ -36,15 +47,19 @@
"test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,06246c96ae9b676262e12828d29a388b"
"versions_genmod": [
[
"GENMOD_ANNOTATE",
"genmod",
"3.10.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2025-04-16T11:25:23.09633885"
"timestamp": "2025-12-22T14:14:43.571171183"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/genmod/compound/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::genmod=3.10.1
- bioconda::genmod=3.10.2
16 changes: 3 additions & 13 deletions modules/nf-core/genmod/compound/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,15 @@ process GENMOD_COMPOUND {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"

input:
tuple val(meta), path(input_vcf)

output:
tuple val(meta), path("*_compound.vcf"), emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -27,21 +27,11 @@ process GENMOD_COMPOUND {
--processes ${task.cpus} \\
--outfile ${prefix}_compound.vcf \\
$input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_compound.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/genmod/compound/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,27 @@ output:
description: Output VCF file
pattern: "*.{vcf}"
ontologies: []
versions_genmod:
- - ${task.process}:
type: string
description: Name of the process
- genmod:
type: string
description: Name of the tool
- "genmod --version | sed 's/^.*genmod version: //'":
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: Name of the process
- genmod:
type: string
description: Name of the tool
- "genmod --version | sed 's/^.*genmod version: //'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@ramprasadn"
maintainers:
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/genmod/compound/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,9 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.vcf.get(0).get(1)).vcf.summary,
).match() }
process.out.findAll { key, val -> key.startsWith("versions") },
).match() }
)
}

Expand Down
40 changes: 27 additions & 13 deletions modules/nf-core/genmod/compound/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,16 +1,22 @@
{
"genmod_compound": {
"content": [
[
"versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
],
"VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]"
"VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]",
{
"versions_genmod": [
[
"GENMOD_COMPOUND",
"genmod",
"3.10.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2025-04-16T11:25:29.069803275"
"timestamp": "2025-12-22T14:47:53.481557902"
},
"genmod_compound - stub": {
"content": [
Expand All @@ -25,7 +31,11 @@
]
],
"1": [
"versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
[
"GENMOD_COMPOUND",
"genmod",
"3.10.2"
]
],
"vcf": [
[
Expand All @@ -36,15 +46,19 @@
"test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
"versions_genmod": [
[
"GENMOD_COMPOUND",
"genmod",
"3.10.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2025-04-16T11:25:34.388372156"
"timestamp": "2025-12-22T14:14:51.229110934"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/genmod/models/environment.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::genmod=3.10.1
- bioconda::genmod=3.10.2
16 changes: 3 additions & 13 deletions modules/nf-core/genmod/models/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,16 @@ process GENMOD_MODELS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"

input:
tuple val(meta), path(input_vcf), path (fam)
path (reduced_penetrance)

output:
tuple val(meta), path("*_models.vcf"), emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,21 +32,11 @@ process GENMOD_MODELS {
--processes ${task.cpus} \\
--outfile ${prefix}_models.vcf \\
$input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_models.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
}
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