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Idea #15406
closed
[cwl] Implement (or just document?) safer bash defaults for CommandLineTools
Status:
Closed
Priority:
Normal
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Category:
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Target version:
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Due date:
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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.
Updated by Tom Morris
Updated by Peter Amstutz over 4 years ago
- Target version deleted (
To Be Groomed) - Status changed from New to Closed
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