Hi channel - has anyone run the pipeline on both broad histone mark ChIP and transcription factor ChIP? I can't find from searching and docs if there's a good way to run the pipeline and call different peak styles for specific samples, or if it's best to submit two separate jobs, one with ChIPs that should have peaks called as narrow peaks, and the other with ChIPs that should have peaks called as broad peaks? Thanks for input!

I’d run the two (broad vs narrow) separately. Basically, I do this any time where the workflow parameters affect each sample and where there may be downstream comparisons between the samples, e.g., consensus peak calls