Update QC report based on CITE-seq post-processing about scpca-nf HOT 3 CLOSED

• TBD: Should this plot only show RNA-based filtering? As written, it will include ADT-based filtering as well, which seems reasonable to me if there are ADT counts! Just need to update text (and maybe make the text conditional)

I think it is fine to show all of the filtering that was applied: I will note though that I think we can just use the values in filtered_sce rather than checking whether they are present from processed_sce? We do put those labels in both SCE files, correct?

• TBD: We end up creating this column if users didn't provide. Do we want to tweak the implementation to add a metadata indicator if this information was user-provided?

I assume you mean the target column here: adding an indicator is fine, but I'm not sure it is needed: the reason to include this info is to indicate how it was used, which I think the column alone does cover.

from scpca-nf.

I think it is fine to show all of the filtering that was applied: I will note though that I think we can just use the values in filtered_sce rather than checking whether they are present from processed_sce? We do put those labels in both SCE files, correct?

💯, will clean this up!

from scpca-nf.

Closed with #343

from scpca-nf.