onecodex-skill

A plugin for AI coding agents (Claude Code, GitHub Copilot CLI, VS Code Copilot Chat, OpenAI Codex) providing the onecodex skill: a reference for the One Codex Python client (samples, analyses, querying, plotting) plus authoring and debugging custom per-sample Workflows on the One Codex platform — shell_script and nextflow job types, runtime contract (env vars, filesystem layout, deinterleave for paired-end FASTQs), dependencies, assets, and gotchas.

The skill follows the Agent Skills open standard, so the same SKILL.md works across tools.

Examples

Some of the tasks you can perform using this skill with an AI coding agent:

• "What's the abundance of E. coli across the samples in my gut-microbiome project?"
• "I want to run Kraken2 with a custom database on every sample I upload."
• "My Nextflow Workflow runs locally but the platform job exits 1 — what am I missing?"
• "Pull all samples uploaded in the last 30 days and dump filename, size, and read count to a CSV."
• "Tag every sample in this project whose top hit is Salmonella enterica with flagged-salmonella."

Install

Claude Code

/plugin marketplace add onecodex-collaborations/onecodex-skill
/plugin install onecodex@onecodex

Update with /plugin marketplace update onecodex.

GitHub Copilot (CLI + VS Code)

Requires the GitHub Copilot CLI (npm install -g @github/copilot).

copilot plugin install onecodex-collaborations/onecodex-skill:plugins/onecodex

Installed globally for your user — available in Copilot CLI and VS Code Copilot Chat across all workspaces. Reload the Copilot Chat view in VS Code after install.

OpenAI Codex CLI

Requires OpenAI Codex CLI ≥ 0.142 (the plugin subcommand isn't in older releases — upgrade with npm install -g @openai/codex@latest).

codex plugin marketplace add onecodex-collaborations/onecodex-skill
codex plugin add onecodex@onecodex

Restart codex and check /skills. (Or do it interactively: codex → /plugins → install.) The OpenAI Codex desktop app picks it up after restart.

Other tools

The skill at plugins/onecodex/skills/onecodex/SKILL.md is plain markdown with frontmatter. Drop it into any tool that reads ~/.claude/skills/, ~/.copilot/skills/, or ~/.agents/skills/.

Local development

Claude Code:

/plugin marketplace add /path/to/onecodex-skill
/plugin install onecodex@onecodex

Copilot CLI:

copilot plugin install ./plugins/onecodex

Update Claude with /plugin marketplace update onecodex; reinstall the Copilot plugin after edits.