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Update parabricks mutectcaller for sarek #11647

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61b9c55
fix: update mutectcaller for sarek
gburnett-nvidia May 14, 2026
22ce59d
chore: update test and snapshot
gburnett-nvidia May 14, 2026
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16 changes: 10 additions & 6 deletions modules/nf-core/parabricks/mutectcaller/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ process PARABRICKS_MUTECTCALLER {
input:
tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals)
tuple val(ref_meta), path(fasta)
tuple val(fai_meta), path(fasta_fai)
path panel_of_normals
path panel_of_normals_index

Expand All @@ -33,9 +34,13 @@ process PARABRICKS_MUTECTCALLER {

def intervals_command = intervals ? (intervals instanceof List ? intervals.collect { interval -> "--interval-file ${interval}" }.join(' ') : "--interval-file ${intervals}") : ""
def prepon_command = panel_of_normals ? "cp -L ${panel_of_normals_index} `readlink -f ${panel_of_normals}`.tbi && pbrun prepon --in-pon-file ${panel_of_normals}" : ""
def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf.gz --in-pon-file ${panel_of_normals} --out-vcf ${prefix}_annotated.vcf.gz" : ""
// pbrun postpon requires uncompressed .vcf input; output uncompressed when PON is provided
def mutect_out = panel_of_normals ? "${prefix}.vcf" : "${prefix}.vcf.gz"
def stats_rename = panel_of_normals ? "mv ${prefix}.vcf.stats ${prefix}.vcf.gz.stats" : ""
def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf --in-pon-file ${panel_of_normals} --out-vcf ${prefix}.vcf.gz" : ""

def num_gpus = task.accelerator ? "--num-gpus ${task.accelerator.request}" : ""
def normal_bam_flag = normal_bam ? "--in-normal-bam ${normal_bam}" : ""
"""
# if panel of normals specified, run prepon
${prepon_command}
Expand All @@ -44,23 +49,22 @@ process PARABRICKS_MUTECTCALLER {
mutectcaller \\
--ref ${fasta} \\
--in-tumor-bam ${tumor_bam} \\
--tumor-name ${meta.tumor_id} \\
--out-vcf ${prefix}.vcf.gz \\
${normal_bam_flag} \\
--out-vcf ${mutect_out} \\
${intervals_command} \\
${num_gpus} \\
${args}

# if panel of normals specified, run postpon
# if panel of normals specified, rename stats and run postpon
${stats_rename}
${postpon_command}
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def postpon_command = panel_of_normals ? "echo '' | gzip > ${prefix}_annotated.vcf.gz" : ""
"""
echo "" | gzip > ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.stats
${postpon_command}

# Capture the full version output once and store it in a variable
pbrun_version_output=\$(pbrun mutectcaller --version 2>&1)
Expand Down
10 changes: 10 additions & 0 deletions modules/nf-core/parabricks/mutectcaller/meta.yml
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Expand Up @@ -61,6 +61,16 @@ input:
description: reference fasta - must be unzipped.
pattern: "*.fasta"
ontologies: []
- - fai_meta:
type: map
description: |
Groovy Map containing reference index information
[ id:'homo_sapiens' ]
- fasta_fai:
type: file
description: reference fasta index - required when input is in CRAM format.
pattern: "*.fai"
ontologies: []
- panel_of_normals:
type: file
description: (Optional) panel of normals file.
Expand Down
30 changes: 21 additions & 9 deletions modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
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Expand Up @@ -16,7 +16,7 @@ nextflow_process {

when {
params {
module_args = "--mutect-low-memory"
module_args = "--tumor-name tumour --mutect-low-memory"
}
process {
"""
Expand All @@ -32,8 +32,12 @@ nextflow_process {
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[2] = [] // pon
input[3] = [] // pon index
input[2] = [ // fasta_fai
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
]
input[3] = [] // pon
input[4] = [] // pon index
"""
}
}
Expand Down Expand Up @@ -100,7 +104,7 @@ nextflow_process {

// when {
// params {
// module_args = "--mutect-low-memory"
// module_args = "--tumor-name tumour --mutect-low-memory"
// }
// process {
// """
Expand Down Expand Up @@ -227,7 +231,7 @@ nextflow_process {

when {
params {
module_args = "--mutect-low-memory"
module_args = "--tumor-name tumour --mutect-low-memory"
}
process {
"""
Expand All @@ -243,8 +247,12 @@ nextflow_process {
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[2] = [] // pon
input[3] = [] // pon index
input[2] = [ // fasta_fai
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
]
input[3] = [] // pon
input[4] = [] // pon index
"""
}
}
Expand Down Expand Up @@ -283,8 +291,12 @@ nextflow_process {
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
input[2] = [ // fasta_fai
[ id: 'reference' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
]
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
"""
}
}
Expand Down
12 changes: 3 additions & 9 deletions modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,7 @@
"id": "test",
"tumor_id": "tumour"
},
[
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
Expand Down Expand Up @@ -51,10 +48,7 @@
"id": "test",
"tumor_id": "tumour"
},
[
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions_parabricks": [
Expand All @@ -70,7 +64,7 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-21T13:36:25.252321993"
"timestamp": "2026-05-14T09:11:19.859893899"
},
"human - bam - stub": {
"content": [
Expand Down
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