RNA-Seq germline variant calling pipeline

[adthrasher]

Add a variant calling pipeline for RNA-Seq. Implements the GATK RNA-Seq short variant discovery best practices workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-).

Adds an implementation of sambamba in WDL.

[a-frantz]

I haven't yet looked at the new sambamba file (or anything "below" that in the GH interface). Will get to it today, but not immediately. Wanted to kick off the feedback I did write.