Parameter for using the --save_reference 'genome' directory

[kaboroevich]

Description of feature

Using the --save_reference parameter retains all the intermediate reference files in the <RESULTS_DIR>/genome directory. However, from my understanding of the parameters documentation, for subsequent runs of the pipeline, each of the reference parameters (--fasta, --gtf, --star_index, --salmon_index, etc.) have to be defined individually. It would be helpful if the path to the genome folder could be provided to a single parameter, such as --use_saved_reference, from which the pipeline would extract the relevant paths.

[drpatelh]

Hi @kaboroevich ! This is a good suggestion and something I have been thinking about to make it easier to re-use the references saved when using --save_reference. The idea with --save_reference has always been to move the genome folder somewhere else for re-use rather than being stored in the results folder for a single experiment. I will see if we can improve this behavior in later releases.

[amizeranschi]

Hi @drpatelh

I tried using the --save_reference option now in nf-core/rnaseq and I noticed that the salmon reference isn't saved in the genome/index/ directory, along with the STAR reference. Is this a bug, or is it by design?

[pinin4fjords]

@amizeranschi I believe I have addressed your comment in #1065

The idea in the OP is good but probably not happening for the next release- bumping to the subsequent.