You only need one configuration file to run the complete workflow. You can use the provided example as starting point. If in doubt read the comments in the config, the documentation of the respective methods and/or try the default values.

configuration (config/config.yaml): Different for every project/dataset and configures the analyses to be performed, specifically the desired methods and their parameters. The fields are described within the file.

Set workflow-specific resources or command line arguments (CLI) in the workflow profile workflow/profiles/default.config.yaml, which supersedes global Snakemake profiles.