The bioBakery help forum

Modifying metaphlan2 options in biobakery workflows

Is there any way of modifying the metaphlan2 default options in biobakery workflows (something like “–strain-profiling-options”)? In particular, I would like to get read counts in addition to relative abundances using “rel_ab_w_read_stats”

Hello, Sorry we don’t currently have a way to modify the default metaphlan2 options in the workflows. That is a great idea though! We will get this added in a future release.

Thanks,
Lauren