PlantAI-dev/skills/gwas-emmax-plot/SKILL.md

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/.