From de5c3266ff63514dc03192b08cac935b07d75f70 Mon Sep 17 00:00:00 2001 From: jemten Date: Thu, 9 Jan 2025 14:13:29 +0100 Subject: [PATCH 1/2] fixing parsing of sex in configs --- conf/modules/call_snv_deepvariant.config | 2 +- conf/modules/generate_cytosure_files.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules/call_snv_deepvariant.config b/conf/modules/call_snv_deepvariant.config index 348e95cc..3bbf2606 100644 --- 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 index 6aab516d..86e1fd01 100644 --- 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(' ') } From 75dc4bc84c140ead00e3e981cddc11ba947a1d7e Mon Sep 17 00:00:00 2001 From: jemten Date: Thu, 9 Jan 2025 14:19:27 +0100 Subject: [PATCH 2/2] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d68b0072..c9223404 100644 --- 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