I've done some work to make the genomic FASTA file optional when you just want quantifications: https://github.com/nf-core/rnaseq/pull/1490. Reasonably major change, so would appreciate review by interested parties. I actually think that for Salmon specifically we should continue supplying the genome FASTA, because it allows for decoy-aware indices, and I've said as much in the documentation updates, but this makes (genomic) FASTA-less operation possible at least.

looking nice