ruff

Author: bpblanken

v03_pipeline/lib/tasks/update_lookup_table.py

@@ -7,7 +7,6 @@
     join_lookup_hts,
     remove_family_guids,
 )
-from v03_pipeline.lib.model import SampleType
 from v03_pipeline.lib.model.constants import PROJECTS_EXCLUDED_FROM_LOOKUP
 from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams
 from v03_pipeline.lib.tasks.base.base_update_lookup_table import (

v03_pipeline/lib/tasks/write_family_table.py

@@ -2,7 +2,6 @@
 import luigi
 import luigi.util
 
-from v03_pipeline.lib.model import SampleType
 from v03_pipeline.lib.paths import family_table_path
 from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams
 from v03_pipeline.lib.tasks.base.base_write import BaseWriteTask

v03_pipeline/lib/tasks/write_imported_callset.py

@@ -16,7 +16,7 @@
     validate_sample_type,
 )
 from v03_pipeline.lib.misc.vets import annotate_vets
-from v03_pipeline.lib.model import CachedReferenceDatasetQuery, SampleType
+from v03_pipeline.lib.model import CachedReferenceDatasetQuery
 from v03_pipeline.lib.model.environment import Env
 from v03_pipeline.lib.paths import (
     cached_reference_dataset_query_path,

v03_pipeline/lib/tasks/write_new_variants_table.py

@@ -11,7 +11,7 @@
 from v03_pipeline.lib.misc.allele_registry import register_alleles_in_chunks
 from v03_pipeline.lib.misc.callsets import get_callset_ht
 from v03_pipeline.lib.misc.math import constrain
-from v03_pipeline.lib.model import Env, ReferenceDatasetCollection, SampleType
+from v03_pipeline.lib.model import Env, ReferenceDatasetCollection
 from v03_pipeline.lib.paths import (
     new_variants_table_path,
     variant_annotations_table_path,

v03_pipeline/lib/tasks/write_project_family_tables.py

@@ -2,7 +2,6 @@
 import luigi
 import luigi.util
 
-from v03_pipeline.lib.model import SampleType
 from v03_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask
 from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams
 from v03_pipeline.lib.tasks.update_project_table import UpdateProjectTableTask

v03_pipeline/lib/tasks/write_relatedness_check_table.py

@@ -3,7 +3,7 @@
 import luigi.util
 
 from v03_pipeline.lib.methods.relatedness import call_relatedness
-from v03_pipeline.lib.model import CachedReferenceDatasetQuery, Env, SampleType
+from v03_pipeline.lib.model import CachedReferenceDatasetQuery, Env
 from v03_pipeline.lib.paths import (
     cached_reference_dataset_query_path,
     relatedness_check_table_path,

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

@@ -15,7 +15,6 @@
 )
 from v03_pipeline.lib.misc.pedigree import parse_pedigree_ht_to_families
 from v03_pipeline.lib.misc.sample_ids import remap_sample_ids, subset_samples
-from v03_pipeline.lib.model import SampleType
 from v03_pipeline.lib.paths import remapped_and_subsetted_callset_path
 from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams
 from v03_pipeline.lib.tasks.base.base_write import BaseWriteTask