Hi Spatial Vi Team, Thank you so much for developing such a useful pipeline! I have a question regarding slide file provisioning for Space Ranger. Since I don’t have internet access on my compute node, I need to manually provide the slide file I downloaded from the 10X Genomics website. I attempted to add it in my params file and as command line arguments using --

spaceranger_slidefile

and also tried

--slidefile

, but I haven’t been able to resolve the issue. Could you recommend the best way to accomplish this? Thank you very much for your time and help! Best regards, Thomas

Hi, Thomas, glad you like the pipeline! There is no specific parameter for

slidefile

, but instead you have to provide it as a per-sample metadata in the samplesheet by adding a

slidefile

column. Please find the details here: https://nf-co.re/spatialvi/dev/docs/usage/#raw-spatial-data