Merge pull request #935 from broadinstitute/relatedness-check-metadata

add relatedness check file path to metadata.json

Author: jklugherz

v03_pipeline/lib/tasks/write_metadata_for_run.py

@@ -4,7 +4,10 @@
 import luigi
 import luigi.util
 
-from v03_pipeline.lib.paths import metadata_for_run_path
+from v03_pipeline.lib.paths import (
+    metadata_for_run_path,
+    relatedness_check_tsv_path,
+)
 from v03_pipeline.lib.tasks.base.base_project_info_params import (
     BaseLoadingRunWithProjectInfoParams,
 )
@@ -52,6 +55,11 @@ def run(self) -> None:
                 'relatedness_check': {},
                 'sex_check': {},
             },
+            'relatedness_check_file_path': relatedness_check_tsv_path(
+                self.reference_genome,
+                self.dataset_type,
+                self.callset_path,
+            ),
         }
         for remapped_and_subsetted_callset in self.input():
             callset_mt = hl.read_matrix_table(remapped_and_subsetted_callset.path)

v03_pipeline/lib/tasks/write_metadata_for_run_test.py

@@ -3,6 +3,7 @@
 import luigi.worker
 
 from v03_pipeline.lib.model import DatasetType, ReferenceGenome, SampleType
+from v03_pipeline.lib.paths import relatedness_check_tsv_path
 from v03_pipeline.lib.tasks.write_metadata_for_run import WriteMetadataForRunTask
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
@@ -70,5 +71,10 @@ def test_write_metadata_for_run_task(self) -> None:
                     },
                     'run_id': 'run_123456',
                     'sample_type': SampleType.WGS.value,
+                    'relatedness_check_file_path': relatedness_check_tsv_path(
+                        ReferenceGenome.GRCh38,
+                        DatasetType.SNV_INDEL,
+                        TEST_VCF,
+                    ),
                 },
             )