You need one configuration file and one annotation file to run the complete workflow. If in doubt read the comments in the config and/or try the default values.
- project configuration (
config/config.yaml): different for every project/dataset and configures the analyses to be performed. - sample annotation (sample_annotation): CSV file consisting of two columns
- name: name of the dataset (tip: keep it short).
- data: absolute path to the Seurat object as .rds.
Set workflow-specific resources or command line arguments (CLI) in the workflow profile workflow/profiles/default.config.yaml, which supersedes global Snakemake profiles.