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

[wzheng0520]

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