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