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This PR is a starting point for the migration of our workflows to use crams from beginning to end. Aside from variable name changes, this PR includes the minimum necessary changes needed to make the somatic_exome workflow use crams; this has been verified with the HCC1395 subset example data, but no further testing has been completed so far.
Several tools are unable to directly work with cram files, and require bam to cram conversion steps in the new version of the pipeline included in this PR:
Several new tools are introduced:
Finally, several tools use docker images that are currently unofficial:
genome
namespace, pending his final approval