@Jim Downie dragging you in-thread. Talked a bit with @James Fellows Yates and @Sam Wilkinson. We think having a --run-fairy switch that won't validate if any one of (Concoct, ComeBin, Semibin) are used, because it becomes useless since Bowtie needs to be run. It would also override Bowtie, so maybe --use-fairy would be more approprirate. It would allow to use mag in a faster "mode" for users with fewer resources and, both by design and fittingly, won't allow the user to run all binners (or ComeBin which is much heavier than all others). I think it's also relevant for users who have quota limitations because it prevents creating a lot of bam files.