Add Arriba (and respective pVACfuse step) to the immuno workflow

[susannasiebert]

This is a rebased version of susannasiebert#1

[tmooney]

This looks good to me (and familiar, too 🙂) Does the arriba case need the star_fusion_file input to be supplied? It's one thing that looks different between the two pvacfuse calls, but maybe that's intentional!

[susannasiebert]

@tmooney This was actually something I was wanting to bring up with @malachig and @chrisamiller. Currently pVACfuse ignores a provided star_fusion_file input when it is run with Arriba data because Arriba provides its own Read Support metrics. However, we could potentially still pull Expression metrics from the star_fusion_file. If we allow a star_fusion_file with Arriba, we need to decide which Read Support data takes precedence.

[susannasiebert]

@tmooney I discussed this with Malachi off-thread and I made a new docker image with added support for arriba with a star fusion file. This PR has been updated to take advantage of this update.

[malachig]

I think all these file names need to be updated to reflect 2.4.0 instead of 2.3.0. It seems the name of the dir AND the file names change when the db is updated