ruff

Author: bpblanken

v03_pipeline/lib/tasks/write_imported_callset.py

@@ -28,17 +28,22 @@
 @luigi.util.inherits(BaseLoadingRunParams)
 class WriteImportedCallsetTask(BaseWriteTask):
     def complete(self) -> luigi.Target:
-        # Handle case where callset was previously imported
-        # with a different sex/relatedness flag.
-        additional_row_fields = get_additional_row_fields(
-            mt,
-            self.reference_genome,
-            self.dataset_type,
-            self.skip_check_sex_and_relatedness,
-        )
-        return super().complete() and all(
-            hasattr(ht, field) for field in additional_row_fields
-        )
+        if super().complete():
+            mt = import_callset(
+                self.callset_path,
+                self.reference_genome,
+                self.dataset_type,
+            )
+            # Handle case where callset was previously imported
+            # with a different sex/relatedness flag.
+            additional_row_fields = get_additional_row_fields(
+                mt,
+                self.reference_genome,
+                self.dataset_type,
+                self.skip_check_sex_and_relatedness,
+            )
+            return all(hasattr(mt, field) for field in additional_row_fields)
+        return False
 
     def output(self) -> luigi.Target:
         return GCSorLocalTarget(