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Bug in cwltool results in packed.cwl but no individual cwl files #36
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jjkoehorst opened this issue
May 23, 2023
· 2 comments
· Fixed by common-workflow-language/cwltool#1847
Closed
Bug in cwltool results in packed.cwl but no individual cwl files #36
jjkoehorst opened this issue
May 23, 2023
· 2 comments
· Fixed by common-workflow-language/cwltool#1847
Comments
@jjkoehorst What is your cwltool version? Can you give me an example I can try out? (I wasn't able to create a reproducer) |
Using the following command and version of cwl
It looks that the workflow finishes nicely but in PROV only packed.cwl is present
The job file:
|
mr-c
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May 26, 2023
… the input object is used. Fixes: ResearchObject/runcrate#36
mr-c
added a commit
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May 26, 2023
… the input object is used. Fixes: ResearchObject/runcrate#36
mr-c
added a commit
to common-workflow-language/cwltool
that referenced
this issue
May 26, 2023
… the input object is used. (#1847) Fixes: ResearchObject/runcrate#36
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Due to a bug in the cwltool (or maybe it is intentional) individual cwl files are missing from the PROV/workflow/ location and only the PROV/workflow/packed.cwl is available. This only happens when you start the workflow with a cwl:tool: argument in the input yaml file.
In theory the packed.cwl should be sufficient or not? Not sure if this is an issue in runcrate but I thought I would let you know.
http://download.systemsbiology.nl/unlock/cwl/issues/PROV_No_CWL.zip (Removed the .DS_Store files).
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