missing test liftover

Author: bpblanken

v03_pipeline/lib/tasks/base/base_loading_run_params.py

@@ -10,11 +10,13 @@ class BaseLoadingRunParams(luigi.Task):
     # but nothing else.
     sample_type = luigi.EnumParameter(enum=SampleType)
     callset_path = luigi.Parameter()
-    imputed_sex_path = luigi.Parameter(
+    # HINT: OptionalParameter vs Parameter is significant here.
+    # The default Parameter will case `None` to the string "None".
+    imputed_sex_path = luigi.OptionalParameter(
         default=None,
         description='Optional path to a tsv of imputed sex values from the DRAGEN GVS pipeline.',
     )
-    filters_path = luigi.Parameter(
+    filters_path = luigi.OptionalParameter(
         default=None,
         description='Optional path to part two outputs from callset (VCF shards containing filter information)',
     )

v03_pipeline/lib/tasks/update_lookup_table_test.py

@@ -7,6 +7,7 @@
 )
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
+TEST_LIFTOVER = 'v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz'
 TEST_VCF = 'v03_pipeline/var/test/callsets/1kg_30variants.vcf'
 TEST_REMAP = 'v03_pipeline/var/test/remaps/test_remap_1.tsv'
 TEST_PEDIGREE_3 = 'v03_pipeline/var/test/pedigrees/test_pedigree_3.tsv'
@@ -26,6 +27,7 @@ def test_skip_update_lookup_table_task(self) -> None:
             project_remap_paths=[TEST_REMAP],
             project_pedigree_paths=[TEST_PEDIGREE_3],
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(uslt_task)
         worker.run()
@@ -57,6 +59,7 @@ def test_update_lookup_table_task(self) -> None:
             project_remap_paths=[TEST_REMAP],
             project_pedigree_paths=[TEST_PEDIGREE_3],
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(uslt_task)
         worker.run()

v03_pipeline/lib/tasks/update_project_table_test.py

@@ -5,6 +5,7 @@
 from v03_pipeline.lib.tasks.update_project_table import UpdateProjectTableTask
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
+TEST_LIFTOVER = 'v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz'
 TEST_VCF = 'v03_pipeline/var/test/callsets/1kg_30variants.vcf'
 TEST_REMAP = 'v03_pipeline/var/test/remaps/test_remap_1.tsv'
 TEST_PEDIGREE_3 = 'v03_pipeline/var/test/pedigrees/test_pedigree_3.tsv'
@@ -22,6 +23,7 @@ def test_update_project_table_task(self) -> None:
             project_remap_path=TEST_REMAP,
             project_pedigree_path=TEST_PEDIGREE_3,
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(upt_task)
         worker.run()

v03_pipeline/lib/tasks/write_family_table_test.py

@@ -5,6 +5,7 @@
 from v03_pipeline.lib.tasks.write_family_table import WriteFamilyTableTask
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
+TEST_LIFTOVER = 'v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz'
 TEST_GCNV_BED_FILE = 'v03_pipeline/var/test/callsets/gcnv_1.tsv'
 TEST_SNV_INDEL_VCF = 'v03_pipeline/var/test/callsets/1kg_30variants.vcf'
 TEST_SV_VCF = 'v03_pipeline/var/test/callsets/sv_1.vcf'
@@ -26,6 +27,7 @@ def test_snv_write_family_table_task(self) -> None:
             project_pedigree_path=TEST_PEDIGREE_3,
             family_guid='abc_1',
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(wft_task)
         worker.run()
@@ -163,6 +165,7 @@ def test_sv_write_family_table_task(self) -> None:
             project_pedigree_path=TEST_PEDIGREE_5,
             family_guid='family_2_1',
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(write_family_table_task)
         worker.run()
@@ -415,6 +418,7 @@ def test_gcnv_write_family_table_task(self) -> None:
             project_pedigree_path=TEST_PEDIGREE_5,
             family_guid='family_2_1',
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(write_family_table_task)
         worker.run()

v03_pipeline/lib/tasks/write_project_family_tables_test.py

@@ -7,6 +7,7 @@
 )
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
+TEST_LIFTOVER = 'v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz'
 TEST_SNV_INDEL_VCF = 'v03_pipeline/var/test/callsets/1kg_30variants.vcf'
 TEST_REMAP = 'v03_pipeline/var/test/remaps/test_remap_1.tsv'
 TEST_PEDIGREE_4 = 'v03_pipeline/var/test/pedigrees/test_pedigree_4.tsv'
@@ -24,6 +25,7 @@ def test_snv_write_project_family_tables_task(self) -> None:
             project_remap_path=TEST_REMAP,
             project_pedigree_path=TEST_PEDIGREE_4,
             validate=False,
+            liftover_ref_path=TEST_LIFTOVER,
         )
         worker.add(write_project_family_tables)
         worker.run()