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) (https://github.com/nf-core/scrnaseq/issues/99)
  • [ ] cellranger multi
• TCR-seq (=RNA+TCR)
  • TRUST4 (https://github.com/nf-core/scrnaseq/issues/71)
  • cellranger vdj
  • cellranger multi
• ATAC-seq (https://github.com/nf-core/scrnaseq/issues/174)
  • [ ] cellranger atac (for only scATAC)
  • [x] cellranger-arc (RNA + ATAC) -> merged in #217
• 10x FFPE protocol (not strictly multimodal, but requires cellranger multi) (https://github.com/nf-core/scrnaseq/issues/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:

• https://github.com/nf-core/scrnaseq/issues/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 #276

[fmalmeida]

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

https://github.com/nf-core/scrnaseq/issues/332