Document nextflow workflow

[wsnoble]

Mike Riffle has made a Nextflow workflow for Casanovo. We need to describe this in the documentation.

See the slack message from July 18th for a version of the text below with hyperlinks.

I think the Nextflow workflow for Casanovo (and optional upload to Limelight) is ready to use. Here are some links to source and information about the workflow. If anyone wants to contribute to any of these, please feel free. If you do try it out, I'd love feedback/suggestions/etc. I'll try this out on the GSIT cluster soon and probably write up a short doc about how to get that going.
Documentation for the workflow: https://nf-ms-dda-casanovo.readthedocs.io/
This describes how to setup, configure, run, and get results from the workflow.
Source code for the workflow: https://github.com/mriffle/nf-ms-dda-casanovo
Code for running all the steps, default configurations, and so on.
Supporting Software:
Casanovo to Limelight XML converter: https://github.com/yeastrc/limelight-import-casanovo
Converts results of a Casanovo search to Limelight XML. Includes source code for the Casanovo parsing and Limelight XML generation.
Casanovo Docker build: https://github.com/mriffle/casanovo-docker
Includes the Dockerfile and script(s) I use to build the Casanovo Docker image used by the workflow.
Limelight "marketing" site: https://limelight-ms.org/
Broad overview of what Limelight is about.