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Contributing to Metagenomics Skills

Thank you for contributing. This repository packages Metagenomics Skills as portable Agent Skills (see agentskills.io and Anthropic Skills): one directory per skill under skills/, plus docs and multi-platform plugin manifests.

Skill structure

skills/
  skill-name/
    SKILL.md                 # required
    agents/openai.yaml       # recommended (Codex UI)
    references/              # optional progressive disclosure
    scripts/                 # optional helpers
    assets/                  # optional templates

Do not add a repository-root references/ tree for skill content. Deep detail belongs inside each skill's own references/ folder.

Required frontmatter

---
name: skill-name
description: >
  What it does. Use this skill when: (1) ..., (2) ..., (3) ...
  For related work, use other-skill.
license: MIT
category: analysis-tools | evaluation | utilities | orchestration
tags: [relevant, tags]
---

Categories

Category Purpose Examples
analysis-tools Core analysis stages preprocessing, basalt
evaluation Metrics and figures mag-qc, visualization
utilities Setup / access setup
orchestration Routing and pipelines tool-selection, metagenomics-workflow

Checklist for new skills

  • SKILL.md under 500 lines
  • Frontmatter complete
  • Cross-links to related skills
  • agents/openai.yaml present
  • Listed in docs/skills.md and plugin-manifest.json
  • No vendor-specific Cursor trailers in commits
  • Works via scripts/install-platforms.sh

Multi-platform

Update manifests if packaging changes:

  • .claude-plugin/marketplace.json
  • .codex-plugin/plugin.json
  • .cursor-plugin/plugin.json
  • plugin-manifest.json
  • docs/multi-platform.md