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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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Add auto chemistry detection for solving mixture of 10X scRNA-Seq chemistries (alevin, kallisto, star) #388

Open wzheng0520 opened 1 week ago

wzheng0520 commented 1 week ago

Description of feature

Hi,

I’d like to implement an auto-detection module to automatically identify the chemistry type for scRNA-seq libraries. This feature would help address scenarios where multiple library chemistries are mixed. By selecting "auto" for the chemistry parameter, the pipeline could perform internal detection to assign the appropriate chemistry type for downstream processing.

Since CellRanger already has an internal function for this, it could also benefit tools like Alevin, Kallisto, and STAR. I’ve developed an internal version based onv2.7.1. Would it be possible to push this as a new branch, or would it be preferable for me to make the updates on the current dev branch to support a future release?

Sincerely Winnie Zheng

grst commented 1 week ago

Dear @wzheng0520,

if you push this into a branch and make a (draft) PR, I am happy to take a look. In principle I am open to such a feature, but in the end I'll need to decide if the additional complexity is worth it. It's always a trade-off between adding new features and ensuring the pipeline is maintainable long-term.

wzheng0520 commented 3 days ago

Hi @grst

Thanks so much, I will push today and let you know once I completed, so you could take time to review it!

Sincerely Winnie Zheng