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Update to topics graphtyper/* #11599

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24 changes: 7 additions & 17 deletions modules/nf-core/graphtyper/genotype/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process GRAPHTYPER_GENOTYPE {
output:
tuple val(meta), path("results/*/*.vcf.gz") , emit: vcf
tuple val(meta), path("results/*/*.vcf.gz.tbi"), emit: tbi
path "versions.yml", emit: versions
tuple val("${task.process}"), val('graphtyper'), eval("graphtyper --help | tail -1 | sed 's/.* //'"), emit: versions_graphtyper, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,30 +32,20 @@ process GRAPHTYPER_GENOTYPE {
printf "$bam_path_text" > bam_list.txt
graphtyper \\
genotype \\
$ref \\
$args \\
${ref} \\
${args} \\
--sams bam_list.txt \\
--threads $task.cpus \\
$region_text

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //')
END_VERSIONS
--threads ${task.cpus} \\
${region_text}
"""

stub:
"""
mkdir -p results/test
echo | gzip > results/test/region1.vcf.gz
echo | gzip > results/test/region2.vcf.gz
echo "" | gzip > results/test/region1.vcf.gz
echo "" | gzip > results/test/region2.vcf.gz
touch results/test/region1.vcf.gz.tbi
touch results/test/region2.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //')
END_VERSIONS
"""

}
48 changes: 32 additions & 16 deletions modules/nf-core/graphtyper/genotype/meta.yml
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Expand Up @@ -8,13 +8,15 @@ keywords:
- pangenome
tools:
- "graphtyper":
description: A graph-based variant caller capable of genotyping population-scale
short read data sets while incorporating previously discovered variants.
description: A graph-based variant caller capable of genotyping
population-scale short read data sets while incorporating previously
discovered variants.
homepage: "https://github.com/DecodeGenetics/graphtyper"
documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide"
tool_dev_url: "https://github.com/DecodeGenetics/graphtyper"
doi: "10.1038/ng.3964"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:Graphtyper
input:
- - meta:
Expand All @@ -29,8 +31,8 @@ input:
ontologies: []
- bai:
type: file
description: BAM index file. This is automatically found base on BAM input file
name
description: BAM index file. This is automatically found base on BAM input
file name
pattern: "*.{bai}"
ontologies: []
- - meta2:
Expand All @@ -50,15 +52,15 @@ input:
e.g. [ id:'genome' ]
- ref_fai:
type: file
description: Reference index file. This is automatically found based on reference
input file name.
description: Reference index file. This is automatically found based on
reference input file name.
pattern: "*.{.fai}"
ontologies: []
- region_file:
type: file
description: File with a list of chromosome/locations in reference genome to genotype.
One region per line in the format <chr>:<start>-<stop>. This or `--region` (in
ext.args) must be specified.
description: File with a list of chromosome/locations in reference genome to
genotype. One region per line in the format <chr>:<start>-<stop>. This or
`--region` (in ext.args) must be specified.
pattern: "*"
ontologies: []
output:
Expand All @@ -84,13 +86,27 @@ output:
description: VCF index file
pattern: "*.{vcf.gz.tbi}"
ontologies: []
versions_graphtyper:
- - ${task.process}:
type: string
description: The name of the process
- graphtyper:
type: string
description: The name of the tool
- graphtyper --help | tail -1 | sed '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
- graphtyper:
type: string
description: The name of the tool
- graphtyper --help | tail -1 | sed 's/.* //':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@zachary-foster"
maintainers:
Expand Down
38 changes: 20 additions & 18 deletions modules/nf-core/graphtyper/genotype/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ nextflow_process {

name "Test Process GRAPHTYPER_GENOTYPE"
script "../main.nf"
config './nextflow.config'
process "GRAPHTYPER_GENOTYPE"

tag "modules"
Expand All @@ -12,12 +13,15 @@ nextflow_process {
test("single - region_file") {

when {
params {
module_args = ""
}
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = [ [ id: 'ref' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[2] = [ [ id: 'ref_index' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
Expand All @@ -32,54 +36,53 @@ nextflow_process {
{ assert snapshot(
process.out.vcf.collect{ meta, vcf -> [ meta, path(vcf[0]).vcf.variantsMD5 ] }, // Second VCF is empty
process.out.tbi,
process.out.versions
process.out.findAll { key, val -> key.startsWith('versions') }
).match() }
)
}

}

test("multiple - region_args") {
config './nextflow.config'
when {
params {
module_args = "--region MT192765.1"
}
process {
"""
input[0] = [
[ id: 'test' ], // meta map
[ id: 'test' ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true) ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true) ]
]
input[1] = [ [ id: 'ref' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[2] = [ [ id: 'ref_index' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = channel.of([])
input[3] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.tbi[0][1]).name,
file(process.out.vcf[0][1]).name, // no variants and header unstable
process.out.versions
).match() }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["vcf", "tbi"])).match() }
)
}

}

test("single - region_file - stub") {
options '-stub'
when {
params {
module_args = ""
}
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = [ [ id: 'ref' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[2] = [ [ id: 'ref_index' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
Expand All @@ -94,7 +97,6 @@ nextflow_process {
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

}
68 changes: 49 additions & 19 deletions modules/nf-core/graphtyper/genotype/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,16 +1,36 @@
{
"multiple - region_args": {
"content": [
"000000001-000029829.vcf.gz.tbi",
"000000001-000029829.vcf.gz",
[
"versions.yml:md5,131488e7eb93b8c761765afcbc51a719"
]
{
"tbi": [
[
{
"id": "test"
},
"000000001-000029829.vcf.gz.tbi"
]
],
"vcf": [
[
{
"id": "test"
},
"000000001-000029829.vcf.gz"
]
],
"versions_graphtyper": [
[
"GRAPHTYPER_GENOTYPE",
"graphtyper",
"2.7.2"
]
]
}
],
"timestamp": "2026-02-14T13:12:02.090140452",
"timestamp": "2026-05-11T22:30:39.050124678",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
"nf-test": "0.9.5",
"nextflow": "26.03.2"
}
},
"single - region_file": {
Expand All @@ -34,14 +54,20 @@
]
]
],
[
"versions.yml:md5,131488e7eb93b8c761765afcbc51a719"
]
{
"versions_graphtyper": [
[
"GRAPHTYPER_GENOTYPE",
"graphtyper",
"2.7.2"
]
]
}
],
"timestamp": "2026-02-16T16:05:22.263192697",
"timestamp": "2026-05-11T22:30:23.400437096",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
"nf-test": "0.9.5",
"nextflow": "26.03.2"
}
},
"single - region_file - stub": {
Expand Down Expand Up @@ -69,15 +95,19 @@
]
]
],
"versions": [
"versions.yml:md5,131488e7eb93b8c761765afcbc51a719"
"versions_graphtyper": [
[
"GRAPHTYPER_GENOTYPE",
"graphtyper",
"2.7.2"
]
]
}
],
"timestamp": "2026-02-14T12:28:22.719581642",
"timestamp": "2026-05-11T22:30:46.904602299",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
"nf-test": "0.9.5",
"nextflow": "26.03.2"
}
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/graphtyper/genotype/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
process {
withName: GRAPHTYPER_GENOTYPE {
ext.args = '--region MT192765.1'
ext.args = params.module_args
}
}
14 changes: 2 additions & 12 deletions modules/nf-core/graphtyper/vcfconcatenate/main.nf
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Expand Up @@ -13,7 +13,7 @@ process GRAPHTYPER_VCFCONCATENATE {
output:
tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf
tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('graphtyper'), eval("graphtyper --help | tail -1 | sed 's/.* //'"), emit: versions_graphtyper, topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -41,11 +41,6 @@ process GRAPHTYPER_VCFCONCATENATE {

# Delete batch VCFs
rm ${prefix}_subset_*.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //')
END_VERSIONS
"""

stub:
Expand All @@ -54,12 +49,7 @@ process GRAPHTYPER_VCFCONCATENATE {
error "Input and output names are the same, set prefix in module configuration to disambiguate!"
}
"""
echo | gzip > ${prefix}.vcf.gz
echo "" | gzip > ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //')
END_VERSIONS
"""
}
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