Basic Exome Alignment +QC Workflow (non-human)

[jasonwalker80]

This replaces #610

[tmooney]

Does this need to be reconciled with https://github.com/genome/analysis-workflows/blob/00313eea071a4199064a565dba2b2802fc9eb429/definitions/subworkflows/qc_exome_no_verify_bam.cwl and the "mouse" pipeline https://github.com/genome/analysis-workflows/blob/00313eea071a4199064a565dba2b2802fc9eb429/definitions/pipelines/exome_alignment_mouse.cwl?

[jasonwalker80]

I suppose exome_alignment_mouse.cwl is the same things... @chrisamiller agree? I had the PR open for a long time, but my forked repo was a mess. It looks like the same workflow except this produces BAM (which is fine given other workflows can still use the pipeline as a sub-workflow and compress to CRAM).

[chrisamiller]

Yeah, based on a quick look, I believe the mouse exome alignment workflow does the same thing:
https://github.com/genome/analysis-workflows/blob/master/definitions/pipelines/exome_alignment_mouse.cwl

Essentially, it drops out bqsr and verify bam id to support non-human species, which is what you're doing here, seems like.