shitshow

bpblanken · bpblanken · commit 89754a415bc4 · 2024-06-12T14:31:41.000-04:00
diff --git a/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py b/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py
@@ -234,7 +234,6 @@ def test_multiple_update_vat(
             BaseUpdateVariantAnnotationsTableTask(
                 reference_genome=ReferenceGenome.GRCh38,
                 dataset_type=DatasetType.SNV_INDEL,
-                sample_type=SampleType.WGS,
             )
         )
         mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_VEP_DATA)
@@ -653,7 +652,6 @@ def test_update_vat_grch37(
             BaseUpdateVariantAnnotationsTableTask(
                 reference_genome=ReferenceGenome.GRCh37,
                 dataset_type=DatasetType.SNV_INDEL,
-                sample_type=SampleType.WGS,
             )
         )
         mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_VEP_DATA)
@@ -719,7 +717,6 @@ def test_update_vat_without_accessing_private_datasets(
             BaseUpdateVariantAnnotationsTableTask(
                 reference_genome=ReferenceGenome.GRCh38,
                 dataset_type=DatasetType.SNV_INDEL,
-                sample_type=SampleType.WGS,
             )
         )
         shutil.rmtree(
@@ -787,7 +784,6 @@ def test_mito_update_vat(
             BaseUpdateVariantAnnotationsTableTask(
                 reference_genome=ReferenceGenome.GRCh38,
                 dataset_type=DatasetType.MITO,
-                sample_type=SampleType.WGS,
             )
         )
         mock_register_alleles.side_effect = None

Original file line number	Diff line number	Diff line change
`@@ -234,7 +234,6 @@ def test_multiple_update_vat(`
`234`	`234`	`BaseUpdateVariantAnnotationsTableTask(`
`235`	`235`	`reference_genome=ReferenceGenome.GRCh38,`
`236`	`236`	`dataset_type=DatasetType.SNV_INDEL,`
`237`		`- sample_type=SampleType.WGS,`
`238`	`237`	`)`
`239`	`238`	`)`
`240`	`239`	`mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_VEP_DATA)`
`@@ -653,7 +652,6 @@ def test_update_vat_grch37(`
`653`	`652`	`BaseUpdateVariantAnnotationsTableTask(`
`654`	`653`	`reference_genome=ReferenceGenome.GRCh37,`
`655`	`654`	`dataset_type=DatasetType.SNV_INDEL,`
`656`		`- sample_type=SampleType.WGS,`
`657`	`655`	`)`
`658`	`656`	`)`
`659`	`657`	`mock_vep.side_effect = lambda ht, **_: ht.annotate(vep=MOCK_VEP_DATA)`
`@@ -719,7 +717,6 @@ def test_update_vat_without_accessing_private_datasets(`
`719`	`717`	`BaseUpdateVariantAnnotationsTableTask(`
`720`	`718`	`reference_genome=ReferenceGenome.GRCh38,`
`721`	`719`	`dataset_type=DatasetType.SNV_INDEL,`
`722`		`- sample_type=SampleType.WGS,`
`723`	`720`	`)`
`724`	`721`	`)`
`725`	`722`	`shutil.rmtree(`
`@@ -787,7 +784,6 @@ def test_mito_update_vat(`
`787`	`784`	`BaseUpdateVariantAnnotationsTableTask(`
`788`	`785`	`reference_genome=ReferenceGenome.GRCh38,`
`789`	`786`	`dataset_type=DatasetType.MITO,`
`790`		`- sample_type=SampleType.WGS,`
`791`	`787`	`)`
`792`	`788`	`)`
`793`	`789`	`mock_register_alleles.side_effect = None`