lint

Author: rxu17

genie/database_to_staging.py

@@ -686,7 +686,7 @@ def filter_out_germline_variants(
     input_data: pd.DataFrame, status_col_str: str
 ) -> pd.DataFrame:
     """Filters out germline variants given a status col str. Genie pipeline
-        cannot have any of these variants. NOTE: We have to search for the 
+        cannot have any of these variants. NOTE: We have to search for the
         status column because there's no column name validation in the release
         steps so the status column may have different casing.
 

tests/test_database_to_staging.py

@@ -142,12 +142,12 @@ def test_store_assay_info_files(syn):
         ),
         (
             pd.DataFrame(
-                dict(SV_Status=["GERMLINE", "SOMATIC"], Sample_ID=["GENIE-1", "GENIE-2"])
+                dict(
+                    SV_Status=["GERMLINE", "SOMATIC"], Sample_ID=["GENIE-1", "GENIE-2"]
+                )
             ),
             "SV_STATUS",
-            pd.DataFrame(
-                dict(SV_Status=["SOMATIC"], Sample_ID=["GENIE-2"])
-            ),
+            pd.DataFrame(dict(SV_Status=["SOMATIC"], Sample_ID=["GENIE-2"])),
         ),
     ],
     ids=["all_germline", "some_germline", "no_germline", "diff_status_col_case"],