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Merged
fellen31 merged 1 commit into from
Dec 10, 2025
Merged

Add index and threads to trgt/merge #9545

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15 changes: 5 additions & 10 deletions modules/nf-core/trgt/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ process TRGT_MERGE {

output:
tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
tuple val(meta), path("*.{tbi,csi}") , emit: index, optional: true
tuple val("${task.process}"), val('trgt'), eval("trgt --version | sed 's/.* //g'"), emit: versions_trgt, topic: versions

when:
Expand All @@ -32,15 +33,11 @@ process TRGT_MERGE {

"""
trgt merge \\
--threads ${task.cpus} \\
$args \\
$reference \\
$output \\
--vcf ${vcfs}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
END_VERSIONS
"""

stub:
Expand All @@ -52,12 +49,10 @@ process TRGT_MERGE {
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def index_type = extension == "vcf.gz" ? "tbi" : extension == "bcf.gz" ? "csi" : ''
def create_index = args.contains("--write-index") && extension.endsWith(".gz") ? "touch ${prefix}.${extension}.${index_type}" : ''
"""
$create_cmd ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
END_VERSIONS
$create_index
"""
}
11 changes: 11 additions & 0 deletions modules/nf-core/trgt/merge/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,17 @@ output:
description: "Merged output file"
pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
ontologies: []
index:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.{tbi,csi}":
type: file
description: "Index of merged output file"
pattern: "*.{tbi,csi}"
ontologies: []
versions_trgt:
- - ${task.process}:
type: string
Expand Down
89 changes: 83 additions & 6 deletions modules/nf-core/trgt/merge/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@ nextflow_process {
path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
path(process.out.vcf.get(0).get(1)).vcf.summary,
path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
process.out.index,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
Expand All @@ -120,6 +121,7 @@ nextflow_process {
path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
path(process.out.vcf.get(0).get(1)).vcf.summary,
path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
process.out.index,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
Expand All @@ -132,6 +134,7 @@ nextflow_process {
input[0] = BCFTOOLS_SORT.out.vcf
.join(BCFTOOLS_SORT.out.tbi)
.first()
.map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
"""
Expand All @@ -143,16 +146,17 @@ nextflow_process {
)
}
}
test("homo sapiens - 1 VCF - --force-single") {
test("homo sapiens - 1 VCF - --force-single --output-type z --write-index") {
when {
params {
trgt_merge_args = "--force-single"
trgt_merge_args = "--force-single --output-type z --write-index"
}
process {
"""
input[0] = BCFTOOLS_SORT.out.vcf
.join(BCFTOOLS_SORT.out.tbi)
.first()
.map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
"""
Expand All @@ -165,11 +169,87 @@ nextflow_process {
path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
path(process.out.vcf.get(0).get(1)).vcf.summary,
path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
process.out.index,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
}
test("homo sapiens - 1 VCF - --force-single --output-type b --write-index") {
when {
params {
trgt_merge_args = "--force-single --output-type b --write-index"
}
process {
"""
input[0] = BCFTOOLS_SORT.out.vcf
.join(BCFTOOLS_SORT.out.tbi)
.first()
.map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.vcf.get(0).get(1)).name,
process.out.index,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
}
test("homo sapiens - 2 VCFs - tbi index - stub") {
options "-stub"
when {
params {
trgt_merge_args = "--output-type z --write-index"
}
process {
"""
input[0] = BCFTOOLS_SORT.out.vcf
.join(BCFTOOLS_SORT.out.tbi)
.map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
.groupTuple()
input[1] = [[],[]]
input[2] = [[],[]]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("homo sapiens - 2 VCFs - csi index - stub") {
options "-stub"
when {
params {
trgt_merge_args = "--output-type b --write-index"
}
process {
"""
input[0] = BCFTOOLS_SORT.out.vcf
.join(BCFTOOLS_SORT.out.tbi)
.map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
.groupTuple()
input[1] = [[],[]]
input[2] = [[],[]]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("homo sapiens - 2 VCFs - stub") {
options "-stub"
when {
Expand All @@ -187,10 +267,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
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