Run CoGAPS followed by SpaceMarkers to find spatially interacting genes in Visium data.
Locally with docker installed (see samplesheet.csv for reference):
nextflow run FertigLab/spatial-pipeline --input [samplesheet] -w [workdir] -profile docker -r main
Other running options - check out profiles in nextflow.config.
Tip
Use --max_memory --max_cpus --max_time to control the maximum resources to grant on the host.