Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

How to handle output files written outside of the cromwell working directory

I need to gather some outputs that are written outside of the cromwell working dir. What’s the best way to approach that? Can I just add a mv statement to my WDL? As far as I can tell, absolute paths to those files won’t work.

For example, cromwell expects output files to be written at a path like /root/workflow_name/uuid/call_name but maybe the actual task writes to /mnt/datastore/foo. The question is, how do you get cromwell to recognize the output files at /mnt/datastore/foo?

Answers

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