Multi-omics support (meta-issue)

[grst]

Description of feature

This issue is to provide an overview of different tools and related sub-issues related to supporting multiple modalities:

• CITE-seq (=RNA+protein) (Add support for CITE-seq data processing #99)
  • cellranger multi
• TCR-seq (=RNA+TCR)
  • TRUST4 (Add TRUST4 for VDJ calling #71)
  • cellranger vdj
  • cellranger multi
• ATAC-seq (Add multiome support (scATAC + scRNA) #174)
  • cellranger atac (for only scATAC)
  • cellranger-arc (RNA + ATAC) -> merged in Cellranger arc #217
• 10x FFPE protocol (not strictly multimodal, but requires cellranger multi) (Support for 10x FFPE scRNA #247)
  • cellranger multi

Seems like support for cellranger multi will get us pretty far!

Once the alignment routes are implemented, we should also make the output of the workflow more user-friendly:

• MuData conversion #292

CC @heylf @fmalmeida

[fmalmeida]

Hi @grst ,
Started running the tool with public data to get the gist of the tool and figure out how to work with the "input csv" for proper implementation.

[fmalmeida]

Using this issue for backup of TODO existing in the implementation of multi-omics analyses.

Here, for the FFPE, related to PR #276

• Discussion here about the simplification of the samplesheet parsing for cellrangermulti to avoid two different parsings.
• Currently, BEAM data is not supported as part of Adding cellrangermulti subworkflow #276

[fmalmeida]

I have added a follow-up issue for the cellranger-multi implementation:

#332