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Update a bunch of args
1 parent 27c6bd8 commit 1840e1e

10 files changed

+46
-18
lines changed

‎v03_pipeline/lib/paths.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -222,8 +222,7 @@ def valid_filters_path(
222222
callset_path: str,
223223
) -> str | None:
224224
if (
225-
not Env.EXPECT_WES_FILTERS
226-
or not dataset_type.expect_filters(sample_type)
225+
not dataset_type.expect_filters(sample_type)
227226
or 'part_one_outputs' not in callset_path
228227
):
229228
return None

‎v03_pipeline/lib/paths_test.py

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -60,22 +60,20 @@ def test_family_table_path(self) -> None:
6060
def test_valid_filters_path(self) -> None:
6161
self.assertEqual(
6262
valid_filters_path(
63-
DatasetType.SNV_INDEL,
63+
DatasetType.MITO,
6464
SampleType.WES,
6565
'gs://bucket/RDG_Broad_WES_Internal_Oct2023/part_one_outputs/chr*/*.vcf.gz',
6666
),
6767
None,
6868
)
69-
with patch('v03_pipeline.lib.paths.Env') as mock_env:
70-
mock_env.EXPECT_WES_FILTERS = True
71-
self.assertEqual(
72-
valid_filters_path(
73-
DatasetType.SNV_INDEL,
74-
SampleType.WES,
75-
'gs://bucket/RDG_Broad_WES_Internal_Oct2023/part_one_outputs/chr*/*.vcf.gz',
76-
),
77-
'gs://bucket/RDG_Broad_WES_Internal_Oct2023/part_two_outputs/*.filtered.*.vcf.gz',
78-
)
69+
self.assertEqual(
70+
valid_filters_path(
71+
DatasetType.SNV_INDEL,
72+
SampleType.WES,
73+
'gs://bucket/RDG_Broad_WES_Internal_Oct2023/part_one_outputs/chr*/*.vcf.gz',
74+
),
75+
'gs://bucket/RDG_Broad_WES_Internal_Oct2023/part_two_outputs/*.filtered.*.vcf.gz',
76+
)
7977

8078
def test_project_table_path(self) -> None:
8179
self.assertEqual(

‎v03_pipeline/lib/tasks/base/base_loading_run_params.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,15 +19,15 @@ class BaseLoadingRunParams(luigi.Task):
1919
parsing=luigi.BoolParameter.EXPLICIT_PARSING,
2020
)
2121
skip_check_sex_and_relatedness = luigi.BoolParameter(
22-
default=True,
22+
default=False,
2323
parsing=luigi.BoolParameter.EXPLICIT_PARSING,
2424
)
2525
skip_expect_filters = luigi.BoolParameter(
26-
default=True,
26+
default=False,
2727
parsing=luigi.BoolParameter.EXPLICIT_PARSING,
2828
)
2929
skip_validation = luigi.BoolParameter(
30-
default=True,
30+
default=False,
3131
parsing=luigi.BoolParameter.EXPLICIT_PARSING,
3232
)
3333
is_new_gcnv_joint_call = luigi.BoolParameter(

‎v03_pipeline/lib/tasks/update_lookup_table_test.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,7 @@ def test_skip_update_lookup_table_task(self) -> None:
2626
], # a project excluded from the lookup table
2727
project_remap_paths=[TEST_REMAP],
2828
project_pedigree_paths=[TEST_PEDIGREE_3],
29+
skip_validation=True,
2930
liftover_ref_path=TEST_LIFTOVER,
3031
)
3132
worker.add(uslt_task)
@@ -57,6 +58,7 @@ def test_update_lookup_table_task(self) -> None:
5758
project_guids=['R0113_test_project'],
5859
project_remap_paths=[TEST_REMAP],
5960
project_pedigree_paths=[TEST_PEDIGREE_3],
61+
skip_validation=True,
6062
liftover_ref_path=TEST_LIFTOVER,
6163
)
6264
worker.add(uslt_task)

‎v03_pipeline/lib/tasks/update_project_table_test.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@ def test_update_project_table_task(self) -> None:
2222
project_guid='R0113_test_project',
2323
project_remap_path=TEST_REMAP,
2424
project_pedigree_path=TEST_PEDIGREE_3,
25+
skip_validation=True,
2526
liftover_ref_path=TEST_LIFTOVER,
2627
)
2728
worker.add(upt_task)

‎v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py

Lines changed: 18 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -164,6 +164,8 @@ def test_missing_pedigree(
164164
project_remap_paths=[TEST_REMAP],
165165
project_pedigree_paths=['bad_pedigree'],
166166
liftover_ref_path=TEST_LIFTOVER,
167+
skip_validation=True,
168+
skip_check_sex_and_relatedness=True,
167169
run_id=TEST_RUN_ID,
168170
)
169171
worker = luigi.worker.Worker()
@@ -197,6 +199,8 @@ def test_missing_interval_reference(
197199
project_remap_paths=[TEST_REMAP],
198200
project_pedigree_paths=[TEST_PEDIGREE_3],
199201
liftover_ref_path=TEST_LIFTOVER,
202+
skip_validation=True,
203+
skip_check_sex_and_relatedness=True,
200204
run_id=TEST_RUN_ID,
201205
)
202206
worker = luigi.worker.Worker()
@@ -364,8 +368,9 @@ def test_multiple_update_vat(
364368
project_guids=['R0113_test_project'],
365369
project_remap_paths=[TEST_REMAP],
366370
project_pedigree_paths=[TEST_PEDIGREE_3],
367-
skip_validation=False,
368371
liftover_ref_path=TEST_LIFTOVER,
372+
skip_validation=False,
373+
skip_check_sex_and_relatedness=True,
369374
run_id=TEST_RUN_ID,
370375
)
371376
worker.add(uvatwns_task_3)
@@ -416,8 +421,9 @@ def test_multiple_update_vat(
416421
project_guids=['R0114_project4'],
417422
project_remap_paths=[TEST_REMAP],
418423
project_pedigree_paths=[TEST_PEDIGREE_4],
419-
skip_validation=False,
420424
liftover_ref_path=TEST_LIFTOVER,
425+
skip_validation=False,
426+
skip_check_sex_and_relatedness=True,
421427
run_id=TEST_RUN_ID,
422428
)
423429
worker.add(uvatwns_task_4)
@@ -688,6 +694,8 @@ def test_update_vat_grch37(
688694
project_remap_paths=[TEST_REMAP],
689695
project_pedigree_paths=[TEST_PEDIGREE_3],
690696
liftover_ref_path=TEST_LIFTOVER,
697+
skip_validation=True,
698+
skip_check_sex_and_relatedness=True,
691699
run_id=TEST_RUN_ID,
692700
)
693701
worker.add(uvatwns_task)
@@ -767,6 +775,8 @@ def test_update_vat_without_accessing_private_datasets(
767775
project_remap_paths=[TEST_REMAP],
768776
project_pedigree_paths=[TEST_PEDIGREE_3],
769777
liftover_ref_path=TEST_LIFTOVER,
778+
skip_validation=True,
779+
skip_check_sex_and_relatedness=True,
770780
run_id=TEST_RUN_ID,
771781
)
772782
worker.add(uvatwns_task)
@@ -824,6 +834,8 @@ def test_mito_update_vat(
824834
project_remap_paths=['not_a_real_file'],
825835
project_pedigree_paths=[TEST_PEDIGREE_5],
826836
liftover_ref_path=TEST_LIFTOVER,
837+
skip_validation=True,
838+
skip_check_sex_and_relatedness=True,
827839
run_id=TEST_RUN_ID,
828840
)
829841
)
@@ -1088,6 +1100,8 @@ def test_sv_update_vat(
10881100
project_remap_paths=['not_a_real_file'],
10891101
project_pedigree_paths=[TEST_PEDIGREE_5],
10901102
liftover_ref_path=TEST_LIFTOVER,
1103+
skip_validation=True,
1104+
skip_check_sex_and_relatedness=True,
10911105
run_id=TEST_RUN_ID,
10921106
)
10931107
)
@@ -1649,6 +1663,8 @@ def test_gcnv_update_vat(
16491663
project_remap_paths=['not_a_real_file'],
16501664
project_pedigree_paths=[TEST_PEDIGREE_5],
16511665
liftover_ref_path=TEST_LIFTOVER,
1666+
skip_validation=True,
1667+
skip_check_sex_and_relatedness=True,
16521668
run_id=TEST_RUN_ID,
16531669
)
16541670
)

‎v03_pipeline/lib/tasks/write_family_table_test.py

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,8 @@ def test_snv_write_family_table_task(self) -> None:
2626
project_remap_path=TEST_REMAP,
2727
project_pedigree_path=TEST_PEDIGREE_3,
2828
family_guid='abc_1',
29+
skip_validation=True,
30+
skip_check_sex_and_relatedness=True,
2931
liftover_ref_path=TEST_LIFTOVER,
3032
)
3133
worker.add(wft_task)
@@ -163,6 +165,8 @@ def test_sv_write_family_table_task(self) -> None:
163165
project_remap_path='not_a_real_file',
164166
project_pedigree_path=TEST_PEDIGREE_5,
165167
family_guid='family_2_1',
168+
skip_validation=True,
169+
skip_check_sex_and_relatedness=True,
166170
liftover_ref_path=TEST_LIFTOVER,
167171
)
168172
worker.add(write_family_table_task)
@@ -415,6 +419,8 @@ def test_gcnv_write_family_table_task(self) -> None:
415419
project_remap_path='not_a_real_file',
416420
project_pedigree_path=TEST_PEDIGREE_5,
417421
family_guid='family_2_1',
422+
skip_validation=True,
423+
skip_check_sex_and_relatedness=True,
418424
liftover_ref_path=TEST_LIFTOVER,
419425
)
420426
worker.add(write_family_table_task)

‎v03_pipeline/lib/tasks/write_metadata_for_run_test.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,8 @@ def test_write_metadata_for_run_task(self) -> None:
2323
project_guids=['R0113_test_project', 'R0114_project4'],
2424
project_remap_paths=[TEST_REMAP_2, TEST_REMAP_2],
2525
project_pedigree_paths=[TEST_PEDIGREE_3, TEST_PEDIGREE_4],
26+
skip_check_sex_and_relatedness=True,
27+
skip_validation=True,
2628
run_id='run_123456',
2729
)
2830
worker.add(write_metadata_for_run_task)

‎v03_pipeline/lib/tasks/write_project_family_tables_test.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,8 @@ def test_snv_write_project_family_tables_task(self) -> None:
2424
project_guid='R0113_test_project',
2525
project_remap_path=TEST_REMAP,
2626
project_pedigree_path=TEST_PEDIGREE_4,
27+
skip_validation=True,
28+
skip_check_sex_and_relatedness=True,
2729
liftover_ref_path=TEST_LIFTOVER,
2830
)
2931
worker.add(write_project_family_tables)

‎v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -82,6 +82,7 @@ def test_write_remapped_and_subsetted_callset_task(
8282
project_guid='R0113_test_project',
8383
project_remap_path=TEST_REMAP,
8484
project_pedigree_path=TEST_PEDIGREE_3,
85+
skip_validation=True,
8586
skip_check_sex_and_relatedness=False,
8687
)
8788
worker.add(wrsc_task)
@@ -115,6 +116,7 @@ def test_write_remapped_and_subsetted_callset_task_failed_sex_check_family(
115116
project_guid='R0114_project4',
116117
project_remap_path=TEST_REMAP,
117118
project_pedigree_path=TEST_PEDIGREE_4,
119+
skip_validation=True,
118120
skip_check_sex_and_relatedness=False,
119121
)
120122
worker.add(wrsc_task)

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