Hi @jessicalmetcalf! We currently don't have support for that in QIIME 2. @gregcaporaso wrote up a post describing how you can use QIIME 1 & 2 to accomplish this (as a workaround). In his post he mentioned that QIIME 2 support will be added in the upcoming 2017.8 release. Things have been re-prioritized in the meantime, so this will likely make it into the next release, 2017.9 (end of September).