Hi, I'm trying to figure out a couple of things from the scdownstream pipeline, but I'm not sure how it works. I want to analyze a dataset that has been collected in a single batch, single lab. I believe I do not need any kind of integration method, however I don't see "integration_method: none" documented. Am I expected to use an empty string there?

Integration method

none

is not possible because the downstream processing steps (clustering, UMAP) all require some kind of embedding to operate on. But you can for example use

pca

as an integration method, which probably best suits your use case

Oh right, I need the some embedding to compute the neighbors! Yes PCA is what I was looking for, thanks!