Story #14888

[CWL] running expression tool on arvados doesn't return proper output

Added by Jiayong Li 23 days ago. Updated 21 days ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

I'm running a workflow (catbeds.cwl) that uses expression tool to get all the bed files from a directory, and then catting them. The workflow works fine.
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-if13mus3rgqopbs

But if I run the expression tool only (getbeds.cwl) https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-95zyqpj0b4k1nuz, it shows the beds as an empty array.

{
    "beds": []
}

This is very confusing when we're testing the expression tool alone.

History

#1 Updated by Jiayong Li 23 days ago

  • Description updated (diff)
  • Target version set to To Be Groomed

#2 Updated by Jiayong Li 23 days ago

  • Description updated (diff)

#3 Updated by Jiayong Li 23 days ago

  • Description updated (diff)

#4 Updated by Peter Amstutz 21 days ago

  • Project changed from Curoverse Support to Arvados

#5 Updated by Peter Amstutz 21 days ago

This is a cwltool bug:

https://github.com/common-workflow-language/cwltool/pull/1075

It'll be fixed in Arvados the next time we refresh cwltool.

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