Hi, first of all thanks a lot for developing this! I was wondering today if I can run Probe Based CytAssist enabled samples on the pipeline, as it complained about the probeset csv missing. Best, Niko

Hi, Niko! Have you specified the probeset file with

--spaceranger_probeset

? This is mentioned in the documentation at https://nf-co.re/spatialvi/dev/parameters/#spaceranger-options.

ahh yes, I somehow skipped some of the available parameters, thanks. I think i’ll wait until you guys have the VisiumHD part implemented, as this makes up the bulk of our requests

No worries, it happens!