Snakebids apps are defined by a config file (snakebids.yml) that specifies which files from a BIDS dataset should be used as input, and the workflow definitions (in one or more Snakefile(s)) that define how to process those input files.

Once Snakebids is installed, to automatically generate a Snakebids project that you can customize to contain your workflow, run snakebids-create and answer the prompts.