Incorporate major changes from single cell dev branch into main

[erflynn]

This (overdue) PR accomplishes three things:
(1) additional nextflow set up options (see PR #60 for details)
(2) adding the fmx_assign_to_gt module (see PR #44 for details)
(3) fixing several bugs in the VDJ process to get it to a working version (which @dtm2451 is currently improving)

The previous PRs have not been resolved because of several key things:

• we have yet to add tests for these new functionalities (I have not had the time to do a deep dive into nf-test)
• the nextflow workflow logic could be cleaner
• there are additional improvements for the nextflow set up that we want to make.

I am proposing we incorporate this into main and move these to-dos to issues because this is a much better working version, even though these are patches. I have confirmed that these changes do not break previous functionality.
What are folks' thoughts here?

[erflynn]

update @dtm2451:
@amadeovezz and I met today to track down the testing error -- it appears that the only difference is that the snapshots now have stdout but did not before, so the tests were failing -- see commit 35ebc24 -- but the outputs of the pipeline are identical. Will go ahead and merge into main tomorrow.