Problems with Harmony k-means calculation

[wlason]

It's a problem with harmonypy so I opened an issue in their repo.
slowkow/harmonypy#10 (comment)

I wonder if adding nclust parameter in pipeline.yaml in the integration workflow might help?

[bio-la]

@wlason can you put in a Pull request with this feature added?
the integration CI will pick it up and test if harmony runs with the additional parameter.

[olivermccallion]

Quick comment to say I ran into this same issue. For me, I had an empty category in my protein modality. Filtering the unused category fixed the issue for me (varying nclust and using Kmeans2 v kmeans didn't)