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snakemake-workflow-engine

77 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a productivity skill usually connects to your mail, calendar or notes.

By stanfish06/skillquarium (GitHub) · productivity · 12 stars · scanned at commit f748ea9

Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.

Works with any agent that supports SKILL.md skills.

What this skill can do

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Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'snakemake-workflow-engine' ] || [ -L ~/.agents/skills/'snakemake-workflow-engine' ]; then echo 'A skill folder named snakemake-workflow-engine already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/stanfish06/skillquarium' "$d" && git -C "$d" checkout --quiet 'f748ea91aa51ce8fc42c27c809dba73a8377b1d5' -- 'skills/snakemake-workflow-engine' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/snakemake-workflow-engine' ~/.agents/skills/'snakemake-workflow-engine' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'snakemake-workflow-engine' ~/.claude/skills/'snakemake-workflow-engine' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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