add germlinecnvcallerflag

Clinical-Genomics · Sep 6, 2024 · bbb7945 · bbb7945
1 parent 359f1ee
commit bbb7945
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py
@@ -103,20 +103,20 @@ def get_target_bed(self, case_id: str, analysis_type: str) -> str:
     def get_germlinecnvcaller_flag(self, analysis_type: str)-> bool:
         if analysis_type == AnalysisType.WHOLE_GENOME_SEQUENCING:
             return True
-        else:
-            return False
+        return False
 
     def get_workflow_parameters(self, case_id: str) -> RarediseaseParameters:
         """Return parameters."""
         analysis_type: AnalysisType = self.get_data_analysis_type(case_id=case_id)
         target_bed: str = self.get_target_bed(case_id=case_id, analysis_type=analysis_type)
+        skip_germlinecnvcaller = self.get_germlinecnvcaller_flag(case_id=case_id, analysis_type=analysis_type)
         return RarediseaseParameters(
             input=self.get_sample_sheet_path(case_id=case_id),
             outdir=self.get_case_path(case_id=case_id),
             analysis_type=analysis_type,
             target_bed=Path(self.references, target_bed).as_posix(),
             save_mapped_as_cram=True,
-            skip_germlinecnvcaller=self.get_germlinecnvcaller_flag(case_id=case_id, analysis_type=analysis_type)
+            skip_germlinecnvcaller=skip_germlinecnvcaller
         )
 
     @staticmethod