Snakemake toy workflow starter

Skill ma-compbio-lab/SkillFoundry/skills/reproducible-workflows/snakemake-toy-workflow-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

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

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

What its author says it does

Copied from the file, not written here

Use this skill to run a tiny Snakemake workflow through the repo-managed Snakemake prefix and inspect deterministic toy outputs.

SKILL.md

2.5 KB, 588 tokens by cl100k_base, as published. Nobody here has run it

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

Provenance

Snakemake documentation: https://snakemake.readthedocs.io/en/stable/
Snakemake installation guide: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
Snakemake tutorial: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html

Related skills

slurm-job-debug-template
scanpy-qc-starter
nextflow-hello-workflow
nf-core-pipeline-list