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CWL 1.0 CT173 Test Docker ENTRYPOINT usage

Open dleehr opened this issue 5 years ago • 5 comments

Got workflow error
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 733, in collect_output
    raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
cwltool.errors.WorkflowException: Did not find output file with glob pattern: '['cow']'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 612, in collect_output_ports
    compute_checksum=compute_checksum)
  File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 733, in collect_output
    raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
  File "/usr/local/lib/python3.6/site-packages/schema_salad/sourceline.py", line 168, in __exit__
    raise self.makeError(six.text_type(exc_value))
cwltool.errors.WorkflowException: v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/cwltool/executors.py", line 264, in runner
    job.run(runtime_context)
  File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 560, in run
    self.finish(completion_result, runtimeContext)
  File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 360, in finish
    outputs = self.collect_outputs(self.outdir)
  File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 612, in collect_output_ports
    compute_checksum=compute_checksum)
  File "/usr/local/lib/python3.6/site-packages/schema_salad/sourceline.py", line 168, in __exit__
    raise self.makeError(six.text_type(exc_value))
cwltool.errors.WorkflowException: Error collecting output for parameter 'cow':
v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']'
Workflow error, try again with --debug for more information:
Error collecting output for parameter 'cow':
v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']'
Test 173 failed: /usr/local/bin/calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8yz5b99m --quiet v1.0/docker-run-cmd.cwl v1.0/empty.json
Test Docker ENTRYPOINT usage
Returned non-zero

dleehr avatar Jul 23 '19 17:07 dleehr