When using the prokaryotic profile, I still got a "stringtie" folder under "bowtie2_salmon" in the output. Does the pipeline use the stringtie data for any purpose? Another question, I set strandedness to "auto" in the sample sheet, so it got inferred by Salmon. I'm not seeing any strandedness assessment in the multiqc report. Where can I find it in the output? Is it in any log?

For bacteria, there is no splicing, i.e. only one transcript per gene. StringTie does not make sense to me here. You could create a GitHub issue and ask for that to be disable in the

prokaryotic

profile.

PR made: https://github.com/nf-core/rnaseq/pull/1804 @Weisheng Wu, are you on GitHub and able to review? You're making lots of useful points and it would be good to have you credited in there. If you're not in the nf-core GitHub org get yourself over to #CEB982K2T 🙂