Update init to copy spark log on failure

broadinstitute · Aug 16, 2024 · ec819a8 · ec819a8
1 parent 09b41f2
commit ec819a8
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/gnomad_qc/v5/data_ingestion/create_vds.py b/gnomad_qc/v5/data_ingestion/create_vds.py
@@ -16,8 +16,11 @@
 def main(args):
     """Create VDS from text file of VDSes or GVCFs paths and write to output path."""
     hl.init(
-        log="/tmp/gvcf_combiner.log", default_reference="GRCh38", tmp_dir=args.temp_path
+        log="/tmp/gvcf_combiner.log",
+        tmp_dir=args.temp_path,
+        copy_spark_log_on_error=True,
     )
+    hl.default_reference("GRCh38")
     vdses = args.vdses
     gvcfs = args.gvcfs
     temp_path = args.temp_path