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[CWL] tries to resolve `File` objects in non-standard extensions

See original GitHub issue

I’m trying to run this workflow using toil-cwl-runner. However, it fails with:

[2020-10-01T08:30:38+0200] [MainThread] [E] [toil.cwl.cwltoil] Got exception 'HTTP Error 404: Not Found' while copying 'https://api.sbgenomics.com/path/to/input_list-1.ext'

It runs fine with cwltool. I am not really sure why is toil even accessing this link, as this is some test link that should always return 404. Is there a known TOIL workarond for such a situation?

┆Issue is synchronized with this Jira Task ┆Epic: CWL v1.2 support ┆Issue Number: TOIL-679

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:15 (9 by maintainers)

github_iconTop GitHub Comments

1reaction
imiloscommented, Oct 28, 2020

Hi @mr-c, just to say that last evening I tried if anything changed since the last pull from the master. It turns out that my workflow started working with the latest commits 😃 I don’t know what exactly has been changed, but thanks a lot for your help and keep going with first-class CWL support!

1reaction
mr-ccommented, Oct 1, 2020

@DailyDreaming That is part of a sbg:job section, which toil-cwl-runner would skip due to the sbg prefix, so I don’t think that is the culprit

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