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Merged
SPPearce merged 1 commit into from
Mar 3, 2026
Merged

Update VCFLIB to topics #10307

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16 changes: 2 additions & 14 deletions modules/nf-core/vcflib/vcfbreakmulti/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ process VCFLIB_VCFBREAKMULTI {

output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('vcflib'), val("1.0.14"), topic: versions, emit: versions_vcflib
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,7 +22,6 @@ process VCFLIB_VCFBREAKMULTI {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}.breakmulti"
def VERSION = '1.0.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

if ( "$vcf" == "${prefix}.vcf.gz" ) {
error "Input and output names are the same, set prefix in module configuration to disambiguate!"
Expand All @@ -32,27 +32,15 @@ process VCFLIB_VCFBREAKMULTI {
$vcf \\
$args \\
| bgzip -c $args2 > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcflib: $VERSION
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}.breakmulti"
def VERSION = '1.0.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

if ( "$vcf" == "${prefix}.vcf.gz" ) {
error "Input and output names are the same, set prefix in module configuration to disambiguate!"
}

"""
echo | gzip > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcflib: $VERSION
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/vcflib/vcfbreakmulti/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,13 +42,27 @@ output:
pattern: "*.vcf.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
versions_vcflib:
- - ${task.process}:
type: string
description: The name of the process
- vcflib:
type: string
description: The name of the tool
- 1.0.14:
type: string
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
- vcflib:
type: string
description: The name of the tool
- 1.0.14:
type: string
description: The expression to obtain the version of the tool
authors:
- "@lucpen"
maintainers:
Expand Down
8 changes: 2 additions & 6 deletions modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith("versions")}
).match()}
)
}
Expand All @@ -53,10 +52,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
47 changes: 18 additions & 29 deletions modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,57 +2,46 @@
"test-vcflib-vcfbreakmulti-stub": {
"content": [
{
"0": [
"vcf": [
[
{
"id": "test"
},
"test.breakmulti.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"versions.yml:md5,6317972d701e04a973fd45e62ae316f1"
],
"vcf": [
"versions_vcflib": [
[
{
"id": "test"
},
"test.breakmulti.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
"VCFLIB_VCFBREAKMULTI",
"vcflib",
"1.0.14"
]
],
"versions": [
"versions.yml:md5,6317972d701e04a973fd45e62ae316f1"
]
},
{
"VCFLIB_VCFBREAKMULTI": {
"vcflib": "1.0.14"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2025-06-27T12:49:33.906407037"
"timestamp": "2026-03-02T22:37:29.367431883"
},
"test-vcflib-vcfbreakmulti": {
"content": [
"bc7bf3ee9e8430e064c539eb81e59bf9",
[
"versions.yml:md5,6317972d701e04a973fd45e62ae316f1"
],
{
"VCFLIB_VCFBREAKMULTI": {
"vcflib": "1.0.14"
}
"versions_vcflib": [
[
"VCFLIB_VCFBREAKMULTI",
"vcflib",
"1.0.14"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2025-06-27T12:49:28.02222234"
"timestamp": "2026-03-02T22:37:23.408482505"
}
}
19 changes: 4 additions & 15 deletions modules/nf-core/vcflib/vcffilter/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ process VCFLIB_VCFFILTER {

output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml", emit: versions
tuple val("${task.process}"), val('vcflib'), val("1.0.14"), topic: versions, emit: versions_vcflib
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,8 +22,7 @@ process VCFLIB_VCFFILTER {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}.filter"
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def VERSION = '1.0.14'

if (!(args.contains("-f") || args.contains("--info-filter") || args.contains("-g") || args.contains("--genotype-filter"))) {
error("VCFLIB_VCFFILTER requires either the -f/--info-filter or -g/--genotype-filter arguments to be supplied using ext.args.")
}
Expand All @@ -34,26 +34,15 @@ process VCFLIB_VCFFILTER {
${args} \\
${vcf} \\
| bgzip -c ${args2} > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcflib: ${VERSION}
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}.filter"
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def VERSION = '1.0.14'

if ("${vcf}" == "${prefix}.vcf.gz") {
error("Input and output names are the same, set prefix in module configuration to disambiguate!")
}
"""
echo | gzip > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcflib: ${VERSION}
END_VERSIONS
"""
}
29 changes: 22 additions & 7 deletions modules/nf-core/vcflib/vcffilter/meta.yml
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Expand Up @@ -12,7 +12,8 @@ tools:
documentation: "https://github.com/vcflib/vcflib"
tool_dev_url: "https://github.com/vcflib/vcflib"
doi: "10.1371/journal.pcbi.1009123"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:vcflib
input:
- - meta:
Expand Down Expand Up @@ -42,13 +43,27 @@ output:
description: Filtered VCF file
pattern: "*.{vcf.gz}"
ontologies: []
versions_vcflib:
- - ${task.process}:
type: string
description: The name of the process
- vcflib:
type: string
description: The name of the tool
- 1.0.14:
type: string
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
- vcflib:
type: string
description: The name of the tool
- 1.0.14:
type: string
description: The expression to obtain the version of the tool
authors:
- "@zachary-foster"
maintainers:
Expand Down
8 changes: 2 additions & 6 deletions modules/nf-core/vcflib/vcffilter/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith("versions")}
).match()}
)
}
Expand Down Expand Up @@ -62,10 +61,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
47 changes: 18 additions & 29 deletions modules/nf-core/vcflib/vcffilter/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,57 +2,46 @@
"test-vcflib-vcffilter": {
"content": [
"86a26a6b691c05bc7f6e74772b44543d",
[
"versions.yml:md5,36cc801e2395c2d163bbd6b0d256e9aa"
],
{
"VCFLIB_VCFFILTER": {
"vcflib": "1.0.14"
}
"versions_vcflib": [
[
"VCFLIB_VCFFILTER",
"vcflib",
"1.0.14"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2025-06-27T12:49:41.69648886"
"timestamp": "2026-03-02T22:37:35.664688194"
},
"test-vcflib-vcffilter-stub": {
"content": [
{
"0": [
"vcf": [
[
{
"id": "test"
},
"test.filter.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"versions.yml:md5,36cc801e2395c2d163bbd6b0d256e9aa"
],
"vcf": [
"versions_vcflib": [
[
{
"id": "test"
},
"test.filter.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
"VCFLIB_VCFFILTER",
"vcflib",
"1.0.14"
]
],
"versions": [
"versions.yml:md5,36cc801e2395c2d163bbd6b0d256e9aa"
]
},
{
"VCFLIB_VCFFILTER": {
"vcflib": "1.0.14"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2025-06-27T13:07:05.523192366"
"timestamp": "2026-03-02T22:37:41.913217791"
}
}
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