@willowblade, it doesn’t have to be published in journal article, but it should be available open source and through a public revision control system such as GitHub. The ideal situation would be if your colleague were interested in making that software available as a QIIME 2 plugin. That would be the quickest way to get the method working in a QIIME 2 environment, and would likely work better as you guys are more familiar with what this needs to do than we are, since we’re not using that protocol.
This document describes what would be involved in writing a QIIME 2 plugin, and we’re available to help with that. If this is a route that you guys are interested in exploring, I’d be happy to answer any questions.