Support for 10x Gem-X V4 libraries

[divyanshusrivastava]

Description of feature

Current version of the pipelien (v2.7.0) runs Cellranger v7, however cellranger v8 is required to process libraries prepared with 10x Gem-X V4 protocol.

Requesting the developers to have cellranger v8 support.
Thanks

[grst]

Should be v8 already, see here:

scrnaseq/modules/nf-core/cellranger/count/main.nf

Line 5 in c8f02f5

container "nf-core/cellranger:8.0.0"

@nick-youngblut is working on 10xV4 support in #348

[grst]

The changes from #348 have been merged. Could you give it a try if you can run the pipeline on your data with the dev version?

[nick-youngblut]

@grst I don't see any docs on SC5P-PE-v3 and SC5P-R2-v3 (CellRanger). Are they currently supported?

[grst]

I would expect that when you specify auto, cellranger would auto-detect the chemistries and run through. Would be great to test that + explicitly add them to the supported protocols though.

[divyanshusrivastava]

Thanks all, it worked for me with the latest pipeline version already. Did not try the dev.
From my end, the issue can be closed !