A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I had a discussion with 10x and atera will have slightly differetly input format than xenium. but only slightly, because of data size. So depending how quickly SpatialData catches up we could decide to either wait for a SpatialData update or implement directly a support for the atera data type bundle.

XR doe also not work for Atera. There will be somethings else. However the something else will be backwards compatible with Xenium.

So far they also not expressed/observed specific Atera artefacts. But it seemed a bit early to make this conclusive.

So at point we should do a meeting do make a decision to either keep (a) one pipeline, perhaps with a different name, (b) two pipelines.

I would prefer option `b` but Iets discuss this further