Add BAM support to Docker wrapper

[jvivian]

The workflow supports BAM, but the Docker wrapper was never updated to reflect that.

[rghu]

do you suggest a workaround until this change is reflected in the Docker wrapper?

[jvivian]

Hi @rghu — do you have a restriction on running the the python version of the workflow? I'm not actually a big fan of the Docker wrapper (I didn't write the initial wrapper and docker-in-docker is a bit messy).