9277: arvados-cwl-runner sets "is_trashed" when directly setting output of container.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 024e9d0861743d2c84327b69cd3b23c4b38ae342..36fe6efbb28ca7be90044e4e2ebd6368a73237ee 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -314,6 +314,10 @@ 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: