Story #15406

[cwl] Implement (or just document?) safer bash defaults for CommandLineTools

Added by Tom Morris 3 months ago. Updated 3 months ago.

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

0%

Estimated time:
Story points:
-

Description

Customer suggestion:

We have a a couple of ShellCommandRequirement CommandLineTool CWLs that basically construct a command like 

bwa | bamSort.

It appears that if the 'bwa' command fails (say, producing empty output), but the end of the pipe doesn't generate an error, Arvados considers the CommandLineTool as "Completed"

It might be good to add an implied 'bash strict mode' for any tools with a ShellCommandRequirement:

I do this sometimes with "set -o pipefail" in my scripts.  

History

#1 Updated by Tom Morris 3 months ago

  • Target version set to To Be Groomed

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