Add support for CITE-seq data processing

[drpatelh]

As suggested by @grst on Slack: "Once we have cellranger, it should also support (10x) cite-seq out-of-the-box. IDK how difficult it would be to support this with the other aligners."

It appears that we already have a modules for cellranger in the dev version of the pipeline.

[rob-p]

Cc'ing @k3yavi who should be able to give good direction for CITE-seq support using alevin-fry. I'll also add the link to the relevant alevin-fry tutorial, though we likely want to update the default protocol here to use USA mode processing in alevin-fry.

[ggabernet]

Hi, I'll work on CITE-seq support using cellranger multi, there are example datasets and I've done this analysis before. For alevin-fry, I'll let someone else with more experience work on it 😄

[grst]

note: when adding CITEseq, the AnnData output should be extended to a corresponding MuData object. See also discussion in #68

[vd4mmind]

Hi, I'll work on CITE-seq support using cellranger multi, there are example datasets and I've done this analysis before. For alevin-fry, I'll let someone else with more experience work on it 😄

Hi @ggabernet , We are starting with NextFlow journey and thanks for making this 10x pipeeline.

Can you let guide if the prod version 2.5.1 has cellranger multi ? We would need to test Chromium GEM-X Single Cell 5' v3 Gene Expression with Feature Barcoding technology, that has Gene Expression (GEX), Feature Barcode Antibody Capture (FB), T cell receptor (TCR), and B cell receptor (BCR).