How to use cwltool:overrides

[ionox0]

I've tried several methods of using cwltool:overrides in my inputs file that is supplied to Toil, but found an error for most methods:

Traceback (most recent call last):
  File "/Users/johnsoni/Desktop/virtualenv/msk/bin/toil-cwl-runner", line 11, in <module>
    sys.exit(main())
  File "/Users/johnsoni/Desktop/virtualenv/msk/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 962, in main
    options, sys.stdin, None, [], options.job_order)
  File "/Users/johnsoni/Desktop/virtualenv/msk/lib/python2.7/site-packages/cwltool/main.py", line 141, in load_job_order
    overrides.extend(resolve_overrides(job_order_object, file_uri(job_order_file), tool_file_uri))
  File "/Users/johnsoni/Desktop/virtualenv/msk/lib/python2.7/site-packages/cwltool/load_tool.py", line 366, in resolve_overrides
    ret, _ = ovloader.resolve_all(ov, baseurl)
  File "/Users/johnsoni/Desktop/virtualenv/msk/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 867, in resolve_all
    val, base_url+subscope, file_base=file_base, checklinks=False)
TypeError: can only concatenate list (not "str") to list

Tried methods:

cwltool:overrides:
  file:///Users/johnsoni/Desktop/code/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl:
    requirements:
    - class: ResourceRequirement
      ramMin: 5000
      coresMin: 1

cwltool:overrides:
  ProcessLoopUMIFastq.cwl:
    requirements:
    - class: ResourceRequirement
      ramMin: 5000
      coresMin: 1

cwltool:overrides:
  "standard_pipeline.cwl":
    requirements:
    - class: ResourceRequirement
      ramMin: 5000
      coresMin: 1

Are there any suggestions for how to provide this as an input in the inputs.yaml file? Thanks!

┆Issue is synchronized with this Jira Story ┆Issue Number: TOIL-246

[DailyDreaming]

@mr-c Is this functionality covered in the current cwl integration tests?

[mr-c]

It is not, as they are an extension to the CWL reference runner and not part of the standard (yet!)

It would be good to have this working in toil-cwl-runner