closes #3821

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 024e9d0861743d2c84327b69cd3b23c4b38ae342..3b14701a9b9480cf6119e6d0e81e478e6da81214 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -11,6 +11,7 @@ import threading
 import hashlib
 import copy
 import json
+import re
 from functools import partial
 import pkg_resources  # part of setuptools
 
@@ -314,6 +315,10 @@ class ArvCwlRunner(object):
                                              body={
                                                  'output': self.final_output_collection.portable_data_hash(),
                                              }).execute(num_retries=self.num_retries)
+                self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
+                                              body={
+                                                  'is_trashed': True
+                                              }).execute(num_retries=self.num_retries)
             except Exception as e:
                 logger.info("Setting container output: %s", e)
         elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
@@ -625,6 +630,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 def add_arv_hints():
     cache = {}
+    cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     cache["http://arvados.org/cwl"] = res.read()
     res.close()