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adding docker and pipefail

Jeff L Froula requested to merge 10-add-docker-to-runtime into cloud2

Closes #10 (closed)

I added set -euo pipefail to most of the command{} sections. Some command{} sections generated non-critical errors (i.e. mv <something_that_doesn't_exist>).

I also added docker: container to most of the runtime{} sections.

The workflow completed successfully, with all tasks turned on, when run in cromwell.jar (not tried in JAWS). I will have my own version that has all JAWS specific runtime params. Hopefully, this version on this branch can be merged and used as the official core WDL.

I didn't touch annotation.wdl only tested annotation_full.wdl.

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