Merge pull request #659 from genomic-medicine-sweden/fix_sex

Fix parsing of sex in config
nf-core · Jan 10, 2025 · da6ee67 · da6ee67
2 parents 41cd7fc + 4a84cb2
commit da6ee67
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 

diff --git a/conf/modules/call_snv_deepvariant.config b/conf/modules/call_snv_deepvariant.config
@@ -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" }
     }

diff --git a/conf/modules/generate_cytosure_files.config b/conf/modules/generate_cytosure_files.config
@@ -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(' ') }