CWL: Bug when using cwltoil (due to overrides?)

[mb1069]

Hi,
I'm experiencing an issue when running my workflow with cwltoil, though it works in cwltool.
The error is:
Traceback (most recent call last): File "/Users/mdb/miniconda2/bin/cwltoil", line 11, in <module> sys.exit(main()) File "/Users/mdb/miniconda2/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1014, in main options, sys.stdin, None, [], options.job_order) File "/Users/mdb/miniconda2/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/mdb/miniconda2/lib/python2.7/site-packages/cwltool/load_tool.py", line 377, in resolve_overrides ret, _ = ovloader.resolve_all(ov, baseurl) File "/Users/mdb/miniconda2/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 871, in resolve_all val, base_url+subscope, file_base=file_base, checklinks=False) TypeError: can only concatenate list (not "str") to list

packed_workflow.txt
pipeline_input.txt

┆Issue is synchronized with this JIRA Story
┆Issue Number: TOIL-327

[DailyDreaming]

I believe this ought to be closed by the same PR fix as #2334.

[mb1069]

Hi,
This issue is still occurring in the latest pull from github (hash 9a38107)
I've gone into the code and found that the base_url used in ref_resolver.resolve_all is a list when the overrides are specified, but is a string in all other cases?

Any help on this would be greatly appreciated!

[mb1069]

resourceRequirementErrorExample.zip

I've created a minimal example,
this works using cwltool --outdir out metaspades.cwl metaspades_paired.yml
but fails when using cwltoil --outdir out metaspades.cwl metaspades_paired.yml

[DailyDreaming]

@mr-c wrote a fix at #2333 that was just merged. @mb1069 can you test this to see if it solves your issue?

[mb1069]

I can confirm the patch works as expected, thank you both for your support!