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common-workflow-library / legacy

Deprecated
https://github.com/common-workflow-library/bio-cwl-tools
Apache License 2.0
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Did you include a $schemas section? #137

Closed evan-wehi closed 7 years ago

evan-wehi commented 7 years ago

Hello,

I'm building a workflow and using CommandLineTool examples from this repository (which are great!). Many have metadata but including them in a workflow produces:

$ ../src/pdx-pl.cwl pdx-inp.yml 
/home/thomas.e/.local/bin/cwl-runner 1.0.20170622090721
Resolved '../src/pdx-pl.cwl' to 'file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl'
No handlers could be found for logger "rdflib.term"
../src/tools/samtools-sort.cwl:66:1: unrecognized extension field `s:downloadUrl`.  Did you include a $schemas section?
../src/tools/samtools-sort.cwl:68:1: unrecognized extension field `s:license`.  Did you include a $schemas section?
../src/tools/samtools-sort.cwl:75:1: unrecognized extension field `s:author`.  Did you include a $schemas section?

This example uses the samtools-sort.cwl directly from the repository (other than commenting out the imports for envvar-global.ylm and samtools-docker.yml)

michael-kotliar commented 7 years ago

It's not the best solution, but you may try to run it with --non-strict flag. It will allow to ignore these warnings

mr-c commented 7 years ago

Hello @evan-wehi

Thank you for reporting your issue. This is a regression in cwltool -- I thought we had documented it already, but evidently not. I'm moving the issue to https://github.com/common-workflow-language/cwltool/issues/455

evan-wehi commented 7 years ago

Thanks for looking at it @mr-c

Evan.

From: Michael R. Crusoe [mailto:notifications@github.com] Sent: 06 July 2017 20:57 To: common-workflow-language/workflows workflows@noreply.github.com Cc: Evan Thomas thomas.e@wehi.edu.au; Mention mention@noreply.github.com Subject: Re: [common-workflow-language/workflows] Did you include a $schemas section? (#137)

Hello @evan-wehihttps://github.com/evan-wehi

Thank you for reporting your issue. This is a regression in cwltool -- I thought we had documented it already, but evidently not. I'm moving the issue to common-workflow-language/cwltool#455https://github.com/common-workflow-language/cwltool/issues/455

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