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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
178 stars 154 forks source link

Use compressed (gzip) fasta and gtf #314

Closed zeehio closed 2 months ago

zeehio commented 2 months ago

Description of feature

It would be nice if the scrnaseq pipeline had a similar/compatible genome preparation as the rnaseq pipeline.

I guess we all lack the time to port and implement it avoiding deduplication.

See:

https://github.com/nf-core/rnaseq/blob/master/subworkflows/local/prepare_genome/main.nf

grst commented 2 months ago

Duplicate of #313

grst commented 2 months ago

Yeah, we should have this here... Do you want to make a PR?

grst commented 2 months ago

It's actually already implemented in #276. Will be fixed once this gets merged.