From 359f1ee144c99e1cc0a0998d4d46d3dc4a11a285 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 6 Sep 2024 17:35:02 +0200
Subject: [PATCH] add germlinecnvcallerflag

---
 cg/meta/workflow/raredisease.py      | 7 +++++++
 cg/models/raredisease/raredisease.py | 1 +
 2 files changed, 8 insertions(+)

diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py
index b8f1e0dd56..921b2cef3d 100644
--- 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
index d3f057d8af..a0a79a42d1 100644
--- 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