Fix some reference data bugs

Author: bpblanken

v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset.py

@@ -64,7 +64,7 @@ def complete(self) -> bool:
             self.dataset_type,
         ):
             datasets_to_check.remove('clinvar')
-            self._datasets_to_update.add('clinvar')
+            self._datasets_to_update.append('clinvar')
 
         annotations_ht_globals = Globals.from_ht(
             hl.read_table(self.output().path),

v03_pipeline/lib/tasks/reference_data/updated_cached_reference_dataset_query.py

@@ -90,10 +90,9 @@ def requires(self) -> luigi.Task:
             UpdatedReferenceDatasetCollectionTask,
         )
 
-        return UpdatedReferenceDatasetCollectionTask(
-            self.reference_genome,
-            self.dataset_type,
-            ReferenceDatasetCollection.COMBINED,
+        return self.clone(
+            UpdatedReferenceDatasetCollectionTask,
+            reference_dataset_collection=ReferenceDatasetCollection.COMBINED,
         )
 
     def create_table(self) -> hl.Table:

v03_pipeline/lib/tasks/reference_data/updated_reference_dataset_collection.py

@@ -60,7 +60,7 @@ def complete(self) -> bool:
             self.dataset_type,
         ):
             datasets.remove('clinvar')
-            self._datasets_to_update.add('clinvar')
+            self._datasets_to_update.append('clinvar')
 
         joined_ht_globals = Globals.from_ht(
             hl.read_table(self.output().path),