# Reference

## Config sections

- `project`
- `trait`
- `[input]`
- `[resources]`
- `[execution]`
- `[output]`

## Output contract

`trait2gene run` writes:

- `metadata/config.snapshot.toml`
- `metadata/run-summary.json`
- `metadata/stage-plan.json`
- `reports/summary.md`
- `reports/index.html` when `execution.write_html = true`