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

MLM Manhattan and QQ plotting skill

Use this skill only for the PlantAI gwas_plot stage.

• Canonical runner: python -m apps.cli.run_gwas_plot
• Dependencies: gwas_mlm
• Inputs: mlm_pvalues, cmlm_pvalues
• Outputs: mlm_manhattan, mlm_qq, cmlm_manhattan, cmlm_qq, manifest, report, environment

Resolve authoritative inputs from successful Manifests before execution. Reject hash, scope, sample-order, 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/.