What is snakemake-toy-workflow-starter?

A small Snakemake workflow that copies sample data and creates a summary file. Snakemake is a tool for defining and running steps in data-processing pipelines.

Use it to inspect a starter workflow, run it locally, and check its deterministic output files.

It provides a clear, repeatable example for testing a scientific pipeline before adapting it to a larger project.

snakemake-toy-workflow-starter — Skill for Claude Code and Codex by ma

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add ma-compbio-lab/SkillFoundry --skill snakemake-toy-workflow-starter

Clone the repo

git clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundry

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter/github.svg)](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter)

Your own site

<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/snakemake-toy-workflow-starter.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 35 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 611 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00035	$0.00611
Opus 5	$0.00017	$0.00305
Sonnet 5	$0.00007	$0.00122
Haiku 4.5	$0.00003	$0.00061

Measured 5d ago against content hash 7d584676c646, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

snakemake-toy-workflow-starter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/check_workflow_layout.py, scripts/run_snakemake_workflow.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/reproducible-workflows/snakemake-toy-workflow-starter/SKILL.md · 64 lines

How it starts

The opening of the file, as written. The whole thing — 64 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Purpose

Provide a small, readable Snakemake workflow that can be executed locally, inspected, and adapted into larger scientific pipelines.

When to use

You need a seed workflow layout for scientific pipeline work.
You want a tiny example before adapting a larger pipeline.

When not to use

You need production-grade workflow packaging or containerization.

Inputs

examples/data/input.txt
examples/config.yaml

Outputs

results/copied.txt
results/summary.json
Optional run summary JSON from the wrapper script

Requirements

The repo-local Snakemake runtime at slurm/envs/snakemake
Local filesystem write access for a scratch workspace

Procedure

Review examples/Snakefile and examples/config.yaml.
Run python3 skills/reproducible-workflows/snakemake-toy-workflow-starter/scripts/check_workflow_layout.py.
Run python3 skills/reproducible-workflows/snakemake-toy-workflow-starter/scripts/run_snakemake_workflow.py --workspace scratch/snakemake-toy-workflow --summary-out scratch/snakemake-toy-workflow/run_summary.json.
Inspect results/copied.txt, results/summary.json, and the wrapper summary JSON.

Validation

Layout script succeeds.
snakemake --version works from the repo-managed prefix.
The workflow completes with --cores 1.
The summary JSON reports the copied toy content and a stable checksum.

Failure modes and fixes

Missing Snakemake: recreate slurm/envs/snakemake.
Wrong working directory: pass absolute or repo-relative paths when invoking Snakemake.
Stale workspace contents: rerun through the wrapper, which reseeds a clean workspace.

Safety and limits

This is a small local workflow only.
It verifies local execution, not cluster submission or containerized workflow deployment.

Examples

python3 .../check_workflow_layout.py
python3 .../run_snakemake_workflow.py --workspace scratch/snakemake-toy-workflow --summary-out scratch/snakemake-toy-workflow/run_summary.json

Read the full file on GitHub · 64 lines

Files

What ships with it

13 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

5d ago First seen · 64 lines · 35 tokens per session scan A 7d584676c646

Subscribe to this mod's changes

snakemake-toy-workflow-starter is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 35 tokens to every session and 611 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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