# EMMAX Manhattan and QQ plotting skill

Use this skill only for the PlantAI `gwas_emplot` stage.

- Canonical runner: `python -m apps.cli.run_gwas_emmax_plot`
- Dependencies: `gwas_emmax`
- Exact input role: `emmax_pvalues` from the successful, identity-matched
  `gwas_emmax` Manifest.
- Scientific outputs: `emmax_manhattan`, `emmax_qq`.
- Evidence outputs: `manifest`, `report`, `environment`.

Resolve only that authoritative Manifest; never scan for a latest association
file or accept caller-selected lineage. Reject hash, scope, or model-lineage
mismatches. Write standard logs, report, environment, Manifest v1, and the
stage-local runner-only reproducibility bundle. Do not copy raw analysis code or
raw underlying tool commands into `final/`.