Pipeline documentation - small adjustments

[Isabelle-b]

Hi all,

Some params are missing or needs small adjustment in the documentation:

• publish_dir > to be added in both 'Full pipeline' and 'Conversion' doc
• output > 'Name or template for the output files', to be added in 'Full pipeline' doc
• Fix incorrectly named filtering arguments in full pipeline #374
• in "CITE-seq filtering options" and "RNA filtering options" sections > all default params need to be added in doc (or 'example' should be changed to 'default') as it is not clear whether they all have default and what default is
• add short description of the Full pipeline output > what is "merged.umap.output.h5mu", or "combined_rna.filter_with_hvg.output.h5mu", "sample_id.filter_with_scrublet.output.h5mu"

Thanks!

[rcannood]

Hi Isabelle!

Thanks for taking the time to create this GitHub issue.

I'm away at a hackathon until next week, but I'll try to look into this issue ASAP.

Robrecht