alternative workflow entry points

[anoronh4]

Description of feature

Clinical would like to run downstream portions of the workflow without repeating time-consuming steps such as alignment or direct interfacing with the fastq. Likely we can do two different entrypoints:

1. Raw fusion calls from arriba, fusioncatcher, and starfusion, and then completing annotation and filtering, etc.
2. Starting with primary bam and proceeding with qc, expression, splicing, etc.