Arvados

bcosca2@lightning-dev1:~/issues/15996/cwl$ arvados-cwl-runner --submit --no-wait --project-uuid=su92l-j7d0g-4i75jw7iivgg3w7 --api=containers --debug gatk-haplotypecaller.cwl testyml/gatk-haplotypecaller.yml 
/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
INFO /usr/bin/arvados-cwl-runner 2.0.0, arvados-python-client 2.0.0, cwltool 1.0.20190831161204
INFO Resolved 'gatk-haplotypecaller.cwl' to 'file:///data-sdc/bcosca2/issues/15996/cwl/gatk-haplotypecaller.cwl'
DEBUG Creating collection reader for 1e488d8a8de69c5e07b447c8e1ae059b+755
DEBUG Creating collection reader for a3af04432df3d71d22f2fe8be549ba96+5974
INFO Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
INFO Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
INFO Using collection cache size 256 MiB
ERROR Unhandled error:
  string indices must be integers, not str
Traceback (most recent call last):
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/main.py", line 833, in main
    logger=_logger)
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 660, in arv_executor
    runnerjob = next(jobiter)
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/future/builtins/newnext.py", line 59, in newnext
    return iterator.next()
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/runner.py", line 649, in job
    self._init_job(job_order, runtimeContext)
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/process.py", line 718, in _init_job
    discover_secondaryFiles=getdefault(runtime_context.toplevel, False)))
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/builder.py", line 276, in bind_input
    bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"], discover_secondaryFiles=discover_secondaryFiles))
  File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/builder.py", line 317, in bind_input
    if "$(" in sf["pattern"] or "${" in sf["pattern"]:
TypeError: string indices must be integers, not str

My CWL is good though...

bcosca2@lightning-dev1:~/issues/15996/cwl$ arvados-cwl-runner --validate gatk-haplotypecaller.cwl 
/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
INFO /usr/bin/arvados-cwl-runner 2.0.0, arvados-python-client 2.0.0, cwltool 1.0.20190831161204
INFO Resolved 'gatk-haplotypecaller.cwl' to 'file:///data-sdc/bcosca2/issues/15996/cwl/gatk-haplotypecaller.cwl'
gatk-haplotypecaller.cwl is valid CWL.