Snakemake — 18 Operations for AI Agents

Snakemake pipelines orchestrate the world's bioinformatics and data workflows — rules, wildcards, DAGs of jobs. act101 reads each rule's inputs and outputs as structure, so agents trace a pipeline without executing it in their head.

This page is the canonical reference an AI coding agent uses to refactor, query, and analyze Snakemake code through the act MCP server. 18 operations available: 0 refactor, 18 query, 0 analysis. Each operation is callable from Claude Code, Cursor, Codex, OpenCode, or any MCP-compatible agent host. Click any operation for a stable anchor link suitable for citation.

Query

18 query tools, the same on every supported language. Descriptions live in the shared reference: /docs/query-tools.

callers control_flow data_flow definition diagnostics effect_closure effect_summary fix_auto get_type graph import_organize interface mutations references repo_outline skeleton symbols symbols_batch