Hi all! New here, so apologies if this has come up before. My team wants to use nf-core/scrnaseq (v4.2.0) with cellranger multi to process multiplexed single-nucleus data from the 10x GEM-X Flex v2 protocol. I don’t see Flex v2 listed under

--protocol

in the usage docs. Since Flex v2 needs Cell Ranger ≥10.0, does anyone know whether 4.2.0 (or the dev branch) supports it? Thanks!

I think cellranger 10 was being added in the dev branch. Maybe it can be ran there using the auto protocol?