Biobakery workflows with metaphlan4 and humann3

Hello:

I would like to know if there is any possibility to use metaphan4 and humann3 in biobakery workflows. I have checked the result using biobakery workflows and metaphlan4 and the second one finds three-four times mor OTUs than the first.

Another possibility is that there is some way to parallelize the analysis of several samples with metaphlan4 and humann3.

Thank you so much