Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. Creates all files (main.nf, module.config, schema.json, nextflow.config, tests) for the common single-tool pattern. Use when asked to add a new bactopia tool, create a bactopia tool, scaffold a complete tool, add a new analysis tool to bactopia-tools, or wire up a bioconda package as a bactopia-tool. This skill handles the full pipeline from package lookup through file generation -- do not use add-module or add-subworkflow separately when the goal is a complete bactopia-tool.
EnglishReview GroovyDoc accuracy across modules and subworkflows using bactopia-lint. Checks @output/@input field matching, @modules/@subworkflows lists, citation keys, tag ordering, and formatting. Use when asked to review GroovyDoc, check documentation accuracy, validate module/subworkflow docs, or audit GroovyDoc.
English
AGENT SKILLS ATLASIncludes Add Bactopia Tool and Review Groovydoc.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Add Bactopia Tool
Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. Creates all files (main.nf, module.config, schema.json, nextflow.config, tests) for the common single-tool pattern. Use when asked to add a new bactopia tool, create a bactopia tool, scaffold a complete tool, add a new analysis tool to bactopia-tools, or wire up a bioconda package as a bactopia-tool. This skill handles the full pipeline from package lookup through file generation -- do not use add-module or add-subworkflow separately when the goal is a complete bactopia-tool.
Review Groovydoc
Review GroovyDoc accuracy across modules and subworkflows using bactopia-lint. Checks @output/@input field matching, @modules/@subworkflows lists, citation keys, tag ordering, and formatting. Use when asked to review GroovyDoc, check documentation accuracy, validate module/subworkflow docs, or audit GroovyDoc.
Quick start
- Choose your skills. Select individual skills above, or choose the entire pack.
- Copy the install prompt. Use Copy install prompt above the list.
- Send it to your agent. Paste into your coding agent’s chat. Your agent reviews the source and guides the setup.
Try it with your agent
After installation, start with a request like:
Use the Add Bactopia Tool skill to help with my task.
Ask me for the context you need before getting started.Requirements & license
- A coding agent that can access your project files and install skills.
- Your agent checks each skill’s instructions, dependencies, and permissions during setup.
- Reported license for the skills shown: MIT. The author’s terms apply.