rna-seq workflow(s) to include differential expression

[d-callan]

tldr: we need our rnaseq workflows to also do differential expression, produce a static plot, and put that plot in the workflow report template. the min req here is that they are updated on brc site, usable by jonathan for broad demo in jan.

Details:

we have two rna-seq workflows in brc site currently, one for paired end data, the other single. neither supports differential expression (de) currently that i know. we do however have a de workflow in iwc already, and i think also some effort during the codeathon from @mvdbeek (correct or clarify me here if im wrong please) to put together an end-to-end workflow for producing both counts matrix and doing de.

we need to use the bits and bobs weve got already to get a workflow in iwc, or update the two workflows from iwc that are already on the site, to support de. ideally these produce a static plot (think de workflow in iwc produces a static volcano plot currently?) that can go in the workflow report template. then the brc site needs updated to include the workflow produced, or use newer versions of existing workflows, as necessary.

important note: not everyone may want to do de, who wants rna-seq. so how to incorporate into brc (multiple workflows? optional subworkflow? etc) needs at least a second or two of thought. given the tight deadline for jan demo, and the idea it should be doable all from brc, multiple workflows as interim measure maybe makes sense, as thats one fewer decision a user has to make within brc (to run subworkflow vs not).

assigning to marius, who can provide clarity on status and path forward hopefully.