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Idea #14888

closed

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

Added by Jiayong Li about 5 years ago. Updated over 4 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Start date:
Due date:
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.

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 #1

Updated by Jiayong Li about 5 years ago

  • Description updated (diff)
  • Target version set to To Be Groomed
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 #2

Updated by Jiayong Li about 5 years ago

  • Description updated (diff)
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 #3

Updated by Jiayong Li about 5 years ago

  • Description updated (diff)
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 #4

Updated by Peter Amstutz about 5 years ago

  • Project changed from 42 to Arvados
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 #5

Updated by Peter Amstutz about 5 years 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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 #6

Updated by Peter Amstutz over 4 years ago

  • Target version deleted (To Be Groomed)
  • Status changed from New to Resolved
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