hinna0818/ukbanalytica_v2/skill-creator

Skill Creator

Purpose

Use this skill to create and maintain repo-bundled Codex skills. Keep every skill concise, triggerable, testable, and safe for UK Biobank RAP workflows.

Workflow

1. Inspect the existing skill tree before editing:

find inst/skills -maxdepth 3 -type f | sort

1. Decide the target:

• New standalone skill: inst/skills/<skill-name>/SKILL.md.
• New UKBAnalytica workflow skill: inst/skills/UKBAnalytica_skills/<ukbsci-name>/SKILL.md.
• Existing skill update: patch only the relevant skill and directly referenced resources.

1. Write SKILL.md first. The frontmatter must contain only:

---
name: lower-hyphen-name
description: Clear trigger description with what the skill does and when to use it.
---

1. Keep the body procedural and short. Put detailed examples, disease catalogs,

function lists, or long checklists in one-hop references/ files.

1. Add resources only when they materially improve reuse:

• references/: detailed guidance loaded only when needed.
• scripts/: deterministic checks or generation utilities.
• assets/: templates or media used in outputs.
• agents/openai.yaml: UI metadata. Its default_prompt must mention $<skill-name>.

1. Validate after edits:

python3 inst/skills/skill-creator/scripts/validate_skill.py inst/skills/<skill-name>

For all repo skills:

python3 inst/skills/skill-creator/scripts/validate_skill.py inst/skills

UKBAnalytica Standards

• Preserve the strict RAP privacy boundary: local agents generate scripts and

interpret aggregate outputs only. They must not read, inspect, summarize, or process real UK Biobank participant-level RAP data or logs containing row values.

• Allow script generation, package guidance, simulated-data smoke tests, and

interpretation of aggregate tables/figures.

• Prefer package functions over ad hoc code in examples.
• Remind users to install or load the latest UKBAnalytica before high-level

workflow examples.

• Add minimal smoke tests when a skill depends on package functions whose

interfaces may change.

Reference Files

Read only the needed reference:

• references/skill-structure.md: SKILL.md, resource layout, and UI metadata.
• references/ukbanalytica-skill-standards.md: UKBAnalytica-specific privacy,

function, and analysis workflow standards.

• references/evaluation-and-smoke-tests.md: validation and smoke-test design.

Completion Checklist

• SKILL.md has valid frontmatter and no placeholder text.
• description contains the trigger conditions.
• Long details are moved into direct references/ files.
• agents/openai.yaml, if present, matches the skill and mentions $skill-name.
• Validation script passes.
• For package-facing skills, a small smoke test exists or the reason for

omitting one is clear.