I have been using q2-itsxpress to extract the its2 region before running dada2. The qiime itsxpress trim-pair-output-unmerged seems to work fine, but the output gives .qza files where the manifest file only contains information for the forward sequences, as discussed in this topic. So I was wondering if there has been some work to fix this.
I was able to replicate this issue, but it was fixed by version 1.7.3 available on Github March 8, 2019.
Unfortunately, I was on the wrong branch when I created the the wheel for version 1.7.3 on Pip. So Pip still has the old version 1.7.2 masquerading as 1.7.3.
I will (carefully) increase the version to 1.7.4 on both Github and pip and let you know. Then you should be able to upgrade with pip.
I need to switch to a better versioning system, maybe Versioneer...