Document valid options for "--genome" parameter

[hendrikweisser]

Description of feature

I find the documentation for the use of reference genomes from iGenomes lacking (see https://nf-co.re/rnaseq/3.9/parameters#reference-genome-options). Apart from "GRCh38", which is mentioned in the extended help text, what other "IDs" are valid for this parameter? And which specific reference genome sources do they map to?

I've looked through a lot of documentation and followed a lot of links (e.g. https://nf-co.re/usage/reference_genomes, https://ewels.github.io/AWS-iGenomes/, https://support.illumina.com/sequencing/sequencing_software/igenome.html), but couldn't find a clear answer.

It may also be helpful to mention where the reference files get downloaded to (I think work/stage/*/* in the output directory), in case they're needed for further analysis.

[hendrikweisser]

It looks like this source file has the relevant information:
https://github.com/nf-core/rnaseq/blob/master/conf/igenomes.config

[drpatelh]

Thanks for reporting!

Docs added in pipeline here: nf-core/website#1501

I re-wrote the main docs on the website to make this clearer in #913. See link below:
https://nf-co.re/usage/reference_genomes#illumina-aws-igenomes