Everything quite calm so far... Is everything going well?

I'll be able to sit down and get to work in around 2 hours, still traveling

@Nico Trummer we (with @Kim Fehl and another teammate) decided to start with some of the issues already exist in your GitHub, specifically PCA integration implementation https://github.com/nf-core/scdownstream/issues/179 For now I don't quite understand the task itself😅 We have different methods of integration 1)gene-based and 2)PCA-based. Am I right, that you what to have "just PCA without integration" option within integration subworkflow? You can provide any thought you have and this will definetly help to understand, what is supposed to be done here :)

Yes, so basically some time ago I was asked how people can use the pipeline if they don't want to use any fancy integration method at all, but just a PCA instead. This is basically it, I think the easiest way of doing it is adding

pca

as an integration method just like

harmony

,

scvi

, etc.