Include CITE-seq processing in docs

[sjspielman]

As part of this Epic https://github.com/AlexsLemonade/scpca-nf/issues/291, we'll need to document processing steps taken for CITE-Seq (ADT) counts, including what those steps were, why we made those choices, and what is now contained in the relevant _processed_sce.rds objects.

Files to update include:

• sce_file_contents.md
• processing_information.md section on CITE-Seq quantification
  • add an additional subsection here to describe post-processing

[sjspielman]

This should probably be tackled in parallel with https://github.com/AlexsLemonade/scpca-nf/issues/293 (add ADT filtering) and https://github.com/AlexsLemonade/scpca-nf/issues/294 (add ADT normalization), at least in terms of getting started in its branch. We may want to break this up into smaller issues, e.g. processing steps vs. SCE object contents. Along these lines, since we are not really planning to use positive controls/spike-ins (if present) during processing, we should include some minimal docs (essentially 1-2 sentences and a link to OSCA) explaining to that users could do processing differently if they wanted to on the unfiltered SCE object.

[sjspielman]

Note to self - send to development branch as we go! Avoids stacking, etc.

[sjspielman]

Note also the final SCE object will now have the output qc data frame from cleanTagCounts() in the CITEseq altexp's colData, if relevant. The columns will differ based on whether there are negative controls, see: https://rdrr.io/github/MarioniLab/DropletUtils/man/cleanTagCounts.html

[sjspielman]

Closed by #110.