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12125: Restore "move trashed items to home" behavior for now.
[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
#!/usr/bin/python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
import arvados
import subprocess
import arvados
import subprocess
@@
-6,6
+9,7
@@
import crunchutil.subst as subst
import shutil
import os
import sys
import shutil
import os
import sys
+import time
if len(arvados.current_task()['parameters']) > 0:
p = arvados.current_task()['parameters']
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
print("arvados-bcbio-nextgen: start writing output to keep")
done = False
+ api = arvados.api('v1')
while not done:
try:
out = arvados.CollectionWriter()
while not done:
try:
out = arvados.CollectionWriter()