Pipeline for processing spatially-resolved gene counts with spatial coordinates, image data, and optionally single cell RNA-seq data, designed for 10x genomics visium and single cell transcriptomics.
Define where the pipeline should find input data and save output data.
Define options for each tool in the pipeline
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.