fix: check whether gCNV is enabled correctly (#357)

bihealth · Jan 18, 2023 · e5ec1b3 · e5ec1b3
1 parent 3bec36b
commit e5ec1b3
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/snappy_pipeline/workflows/common/gcnv/gcnv_run.py b/snappy_pipeline/workflows/common/gcnv/gcnv_run.py
@@ -516,7 +516,9 @@ def get_result_files(self):
 
         The function will skip pedigrees where samples have inconsistent library kits and print a warning.
         """
-        if "gcnv" not in self.config["tools"] and "gcnv" not in self.config["tools"].get("dna", {}):
+        if "gcnv" not in self.config["tools"] and not (
+            hasattr(self.config["tools"], "get") and "gcnv" in self.config["tools"].get("dna", {})
+        ):
             return
 
         # Get list with all result path template strings.

diff --git a/snappy_pipeline/workflows/common/sv_calling.py b/snappy_pipeline/workflows/common/sv_calling.py
@@ -18,7 +18,8 @@ def get_result_files(self):
         returned by ``self.get_output_files()`` for all actions in ``self.actions``.
         """
         if self.name not in self.config["tools"] and not (
-            hasattr(self.config, "tools") and self.name in self.config["tools"].get("dna", {})
+            hasattr(self.config["tools"], "get")
+            and self.name in self.config["tools"].get("dna", {})
         ):
             return  # tool not enabled, no result files