Advanced configuration¶

This guide describes advanced configuration methods.

Environment variables and `.env` files¶

Some CLI options, such as --layout, can be configured via environment variables. This will be indicated in the usage message when running nipoppy <SUBCOMMAND> --help.

It is also possible to set these options using .env environment files. Nipoppy searches the following locations (in order of decreasing priority):

<NIPOPPY_PROJECT_ROOT>/.env: project-level
~/.nipoppy/.env: user-level

The overall order for determining the value of options is as follows (highest to lowest priority):

Command-line options that are explicitly passed when calling the command
Environment variables that are already defined at runtime
Environment variables loaded from .env file(s) (see above)
CLI default values