Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>

[arvados.git] / crunch_scripts / arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index c2962483999b04cad29d7e20ef06e508240cdb36..b7e19ecddb67061b3addde4a82e8a4a59c969202 100755 (executable)
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -1,4 +1,7 @@
 #!/usr/bin/python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
 
 import arvados
 import subprocess
@@ -6,6 +9,7 @@ import crunchutil.subst as subst
 import shutil
 import os
 import sys
+import time
 
 if len(arvados.current_task()['parameters']) > 0:
     p = arvados.current_task()['parameters']
@@ -121,6 +125,7 @@ if rcode == 0:
     print("arvados-bcbio-nextgen: start writing output to keep")
 
     done = False
+    api = arvados.api('v1')
     while not done:
         try:
             out = arvados.CollectionWriter()