Facilitate running the rnaseq pipeline on prokaryotic samples

[MatthiasZepper]

Description of feature

Once in the while, people on Slack ask about issues they encounter when running the rnaseq pipeline on prokaryotic RNA samples. Part of the confusion arises from the completely outdated documentation (separate issue #1084), but there is also room for some technical improvements to the pipeline code.

Ultimately, the goal would be to simplify running the pipeline on prokaryotic samples (e.i. those whose annotation does adhere to the canonical trinity of exon -> transcript -> gene).

I think, this could be a suitable Hackathon task for more advanced nf-core contributors:

• Reproduce the issue reported in this Slack thread. Suitable E.coli RNA-seq data can e.g. be found in GSE183363 or GSE242875.
• Read through the summary written by Marine Cambon describing the steps necessary to run recent pipeline versions on prokaryotic data. Mind specifically steps that required manual changes to the reference files or providing custom configs to the tools.
• Adapt the pipeline, primarily the prepare_genome.nf subworkflow, to handle also prokaryotic references properly. Possibly, introduce a new parameter to make the switch between eukaryotic and prokaryotic analyses.

Thanks!