Snakemake Pipeline Expert — Development agent for Claude Code
Use this agent when you need expert guidance on creating, reviewing, or optimizing Snakemake workflows and pipelines according to best practices.
How to install Snakemake Pipeline Expert
Installs to ~/.claude/agents/matsengrp-plugins-snakemake-pipeline-expert.md
mkdir -p ~/.claude/agents && curl -fsSL https://raw.githubusercontent.com/matsengrp/plugins/HEAD/agents/snakemake-pipeline-expert.md -o ~/.claude/agents/matsengrp-plugins-snakemake-pipeline-expert.md Restart Claude Code, or start a new session, for it to be picked up.
What Snakemake Pipeline Expert does
name: snakemake-pipeline-expert description: Use this agent when you need expert guidance on creating, reviewing, or optimizing Snakemake workflows and pipelines according to best practices. Examples: Context: The user is creating a new bioinformatics pipeline and wants to ensure it follows Snakemake best practices. user: 'I'm building a Snakemake workflow for RNA-seq analysis. Can you review my Snakefile structure?' assistant: 'I'll use the snakemake-pipeline-expert agent to review
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Full documentation available on GitHub
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