Snakebids apps rely on a configuration file (snakebids.yml). This file specifies which files from a BIDS dataset should be used as input. The apps also utilize workflow definitions, which are written in one or more Snakefile(s) and determine how the input files are processed.


For an easy setup of new Snakebids apps with convenient command-line functions, we recommend installing Snakebids using pipx. Visit the following page for instructions on how to install pipx.

Once Snakebids is installed, you can generate a customized Snakebids project by running the command snakebids create and providing the necessary information when prompted.