add germlinecnvcallerflag

Clinical-Genomics · Sep 6, 2024 · 359f1ee · 359f1ee
1 parent f429b92
commit 359f1ee
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Showing 2 changed files with 8 additions and 0 deletions.
diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py
@@ -100,6 +100,12 @@ def get_target_bed(self, case_id: str, analysis_type: str) -> str:
             raise ValueError("No capture kit was found in LIMS")
         return target_bed
 
+    def get_germlinecnvcaller_flag(self, analysis_type: str)-> bool:
+        if analysis_type == AnalysisType.WHOLE_GENOME_SEQUENCING:
+            return True
+        else:
+            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)
@@ -110,6 +116,7 @@ def get_workflow_parameters(self, case_id: str) -> RarediseaseParameters:
             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)
         )
 
     @staticmethod

diff --git a/cg/models/raredisease/raredisease.py b/cg/models/raredisease/raredisease.py
@@ -67,3 +67,4 @@ class RarediseaseParameters(WorkflowParameters):
     target_bed: str
     analysis_type: str
     save_mapped_as_cram: bool
+    skip_germlinecnvcaller: bool