WriteNewVariantsTable is a new task which inherits from BaseWriteTask. It identifies new variants from the callset, annotates them with rdc annotations, and writes to a new table.
UpdateVariantAnnotationsTableWithNewSamplesTask now requires WriteNewVariantsTable and instead of joining variants from the callset directly it joins from variants from the new variants table. vep still runs here.
The new task is covered in existing tests in update_variant_annotations_table_with_new_samples_test.py because I didn't mock the dependency.
WriteNewVariantsTableis a new task which inherits from BaseWriteTask. It identifies new variants from the callset, annotates them with rdc annotations, and writes to a new table.UpdateVariantAnnotationsTableWithNewSamplesTasknow requiresWriteNewVariantsTableand instead of joining variants from the callset directly it joins from variants from the new variants table. vep still runs here.The new task is covered in existing tests in
update_variant_annotations_table_with_new_samples_test.pybecause I didn't mock the dependency.