Hi all, is there a parameter or setting to perform fastqc / multiQC on the reads after rRNA removal. Could be useful to see differences after filtering this way.

I don't think this possible directly. FastQC is already run twice, before and after trimming, automatically. You are making a good point that the 2nd FastQC run could be done after removing rRNA (and any contaminants with BBSplit) -- you could open an issue on GitHub to discuss this. (I would expect this to affect e.g. the GC content For now, you would have to run FastQC manually (not hard to do), and I believe the parameter

--save_non_ribo_reads

should be helpful for that, since it would save those FASTQs to be used as input.

We have a feature request for this, I'll try and implement it soon https://github.com/nf-core/rnaseq/issues/1276

Thanks for implementing this so quickly!