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fix check for panel of normals and add in log #319

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fix check for panel of normals and add in log #319

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f156adf
fix check for panel of normals and add in log
sorelfitzgibbon Oct 25, 2024
ce9aeac
update changelog
sorelfitzgibbon Oct 25, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add option to input VCFs for intersection
- Add VAF stripplot for variant overlaps across tools

### Fixed
- Avoid warning when run without panel of normals

## [8.1.0] - 2024-05-15

### Added
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3 changes: 3 additions & 0 deletions config/methods.config
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Expand Up @@ -92,6 +92,9 @@ methods {
params.germline = false
}
params.germline_resource_gnomad_vcf_index = "${params.germline_resource_gnomad_vcf}.tbi"
if (!params.containsKey("panel_of_normals_vcf")) {
params.panel_of_normals_vcf = ""
}
}

check_valid_algorithms = {
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5 changes: 3 additions & 2 deletions module/mutect2-processes.nf
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Expand Up @@ -15,6 +15,7 @@ Mutect2 Options:
- single tumor normal pair: ${params.single_NT_paired}
- germline resource: ${params.germline_resource_gnomad_vcf}
- contamination_table: ${params.input.tumor.contamination_table}
- panel of normals: ${params.panel_of_normals_vcf}
"""

process run_SplitIntervals_GATK {
Expand Down Expand Up @@ -92,7 +93,7 @@ process call_sSNV_Mutect2 {
normal_names = normal_name.collect { "-normal ${it}" }.join(' ')
bam = normal_names == '-normal NO_ID' ? "$tumors" : "$tumors $normals $normal_names"
germline = params.germline ? "--germline-resource $germline_resource_gnomad_vcf" : ""
panel_of_normals = params.panel_of_normals_vcf ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""
panel_of_normals_cmd = params.panel_of_normals_vcf ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""
interval_id = interval.baseName.split('-')[0]
"""
set -euo pipefail
Expand All @@ -105,7 +106,7 @@ process call_sSNV_Mutect2 {
-O ${params.output_filename}_unfiltered-${interval.baseName}.vcf.gz \
--tmp-dir \$PWD \
$germline \
$panel_of_normals \
$panel_of_normals_cmd \
${params.mutect2_extra_args}
"""
}
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