TypeError: unhashable type: 'CommentedSeq'

I get following error when running one of my CWL workflow with toil 3.13.0:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/toil/worker.py", line 316, in main
    job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
  File "/usr/local/lib/python2.7/dist-packages/toil/job.py", line 1323, in _runner
    returnValues = self._run(jobGraph, fileStore)
  File "/usr/local/lib/python2.7/dist-packages/toil/job.py", line 1268, in _run
    return self.run(fileStore)
    shortname(inp["source"]), promises[inp["source"]].rv())
  File "/usr/local/lib/python2.7/dist-packages/cwltool/process.py", line 170, in shortname
    d = urllib.parse.urlparse(inputid)
  File "/usr/lib/python2.7/urlparse.py", line 143, in urlparse
    tuple = urlsplit(url, scheme, allow_fragments)
  File "/usr/lib/python2.7/urlparse.py", line 176, in urlsplit
    cached = _parse_cache.get(key, None)
TypeError: unhashable type: 'CommentedSeq'

For older versions of toil I get:

 Traceback (most recent call last):
  File "/usr/local/bin/cwltoil", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/toil/cwl/cwltoil.py", line 876, in main
    job = cwltool.main.load_job_order(options, t, sys.stdin)
TypeError: load_job_order() takes exactly 5 arguments (3 given)

With the cwltool it works, though.

Has someone an idea what went wrong?

[mr-c]

We recently fixed cwltool to accept this, so toil needs to update its cwltool dependency to gain the fix.

[ghost]

@mr-c which version of cwltool fixes this? Thanks! I’m getting this error with the current release of Toil which has the cwltool requirement 1.0.20180518123035. Could I be running into something else? Thanks!