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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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Allow pre-built cellranger index, CellrangerARC index, simpleaf Index, and simpleaf tx2pgene load from igenomes.json #371

Closed wzheng0520 closed 2 weeks ago

wzheng0520 commented 2 months ago

Description of feature

Hi guys,

Right now, I found for cellranger index, simpleaf index and simpleaf tx2pgene, the only way we can provide the pre-built indices is through using --cellranger_index, --salmon_index and --txp2gene parameters. I am thinking about if we already have the default path of those pre-built indices, once we use our own igenomes.config file, those indices should be directly pull from there like fasta, gtf, or star_index right now in the pipeline.

I think if it is possible to add following lines before we defined their channel in the scrnaseq.nf

params.salmon_index = getGenomeAttribute('simpleaf')
params.txp2gene = getGenomeAttribute('simpleaf_tx2pgene')
params.cellranger_index = getGenomeAttribute('cellranger')

to allow the pipeline can capture the those information directly from igenomes.config if the --genome we provided have those information.

Sincerely Winnie Zheng

FelixKrueger commented 1 month ago

I would like to second this. It doesn't make sense to re-run all indexing processes for every single run when they are already part of the genome config file. This should also be cut down noticeably the execution time, and the carbon footprint!

FelixKrueger commented 2 weeks ago

Tagging @apeltzer. This would be good to add, I believe we've got this internally already.

FelixKrueger commented 2 weeks ago

I have opened a PR for this (see link above), I think we can close this issue.