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Fix sex #659

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Jan 10, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
- Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)
- Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0 [#643](https://github.com/nf-core/raredisease/pull/643)
- Fixed issue of parsing sample sex in the configs [#659](https://github.com/nf-core/raredisease/pull/659)

### Parameters

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2 changes: 1 addition & 1 deletion conf/modules/call_snv_deepvariant.config
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ process {
withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT' {
ext.args = { [
"--model_type=${params.analysis_type.toUpperCase()}",
meta.sex == "1" ? params.genome == 'GRCh37' ? '--haploid_contigs="X,Y"' : '--haploid_contigs="chrX,chrY"' : ''
meta.sex == 1 ? params.genome == 'GRCh37' ? '--haploid_contigs="X,Y"' : '--haploid_contigs="chrX,chrY"' : ''
].join(' ') }
ext.prefix = { "${meta.id}_deepvar" }
}
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2 changes: 1 addition & 1 deletion conf/modules/generate_cytosure_files.config
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ process {

withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' {
ext.args = { [
meta.sex.equals('1') ? '--sex male' : '--sex female',
meta.sex == 1 ? '--sex male' : '--sex female',
'--size 5000',
'--maxbnd 5000'
].join(' ') }
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