Is there any way to turn off fastqc in /mag ? imo fastp does a pretty good job at producing a before/after report, and the bowtie logs contain plenty of info for multiqc to aggregate a good report. Couldn't find a switch in parameters.

No, currently we don't have an option to turn it off.

But we could do, feel free to make an issue 🙂

sounds like my first ever quest in nf-coreland, exciting

😬 how deep into the rabbit hole do you want to go?

yes that's what I meant haha. gotta have something to do while my thesis is being evaluated...