Recently came across the paper for the duplicate read marking tool FastDup (https://doi.org/10.1093/bioinformatics/btaf633) and thought it could potentially be useful in this pipeline. At least in my hands, MarkDuplicates seems to be a big bottleneck in the pipeline, so having a faster tool could be handy!

Seems interesting to me. If you are up for it you could try and create the nf-core/module for it and then we can work on integrating it into the pipeline?