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Unless you want to handwire something together or use another higher level function from some 3rd party library, your want to use this function. It is basically the entrypoint to a flake based nixos system configuration. See https://github.com/NixOS/templates/blob/master/simple-container/flake.nix for an example.
The arguments can be found here https://github.com/NixOS/nixpkgs/blob/master/nixos/lib/eval-config.nix but system and modules are the only two arguments you need for now. There is probably some documentation in the manual but there is no API documentation.