Running 'cellranger-arc count' with existing genome index

nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

https://nf-co.re/scrnaseq

MIT License

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Running 'cellranger-arc count' with existing genome index #331

Open ashwinikumarkulkarni opened 1 month ago

ashwinikumarkulkarni commented 1 month ago

Description of feature

Current version 2.6.0 does not allow running 'cellranger-arc count' with existing genome index. It keeps asking for 'genome' and 'gtf'. Also, it does not recognize '--cellranger_index' as a parameter when '--aligner' is set to 'cellrangerarc'. Thanks!