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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Support for 10x Gem-X V4 libraries #349

Closed divyanshusrivastava closed 1 month ago

divyanshusrivastava commented 1 month ago

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 commented 1 month ago

Should be v8 already, see here: https://github.com/nf-core/scrnaseq/blob/c8f02f515d014ee2c98b401950e2cf7141a82b42/modules/nf-core/cellranger/count/main.nf#L5

@nick-youngblut is working on 10xV4 support in https://github.com/nf-core/scrnaseq/pull/348

grst commented 1 month ago

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 commented 1 month ago

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

grst commented 1 month ago

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 commented 1 month ago

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 !