Allow pre-built indexes load from igenomes.json and refgenie

[maciekmigdal]

Description of feature

This feature request is to re-introduce feature described in #371, shortly it is to allow the pipeline capture --cellranger_index, --salmon_index and --txp2gene directly from custom igenomes.config when --genome argument is specified. While cellranger index, salmon index, txp2gene are not available in iGenomes, it is valid to accept them from custom igenomes.config. Moreover, if using refgenie these are currently ignored as well.

To enable this following lines (or similar) should be added to scrnaseq.nf

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

See #371 for implementation details.

[maciekmigdal]

There are other indexes that could benefit from being added to scrnaseq.nf eg. kallisto index