Hey @Stef!
Yep! I wasn't as clear as I should've been in my initial reply:
The ignore_missing_samples flag have been added to:
The param can be used by directly running one of those q2-emperor commands directly. That parameter has not been exposed in the diversity core-metrics or diversity core-metrics-phylogenetic pipelines, and I don't think we are currently planning on making that change, since it is so specific to q2-emperor. If you want to take advantage of that new parameter, you can run the constituent commands on their own, remembering to supply the ignore_missing_samples flag as appropriate. Since you are asking about emperor specifically, you can skip all of the alpha steps and skip straight to the beta metrics.
:qiime2: 