Snakemake toy workflow starter

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

1. Review examples/Snakefile and examples/config.yaml.
2. Run python3 skills/reproducible-workflows/snakemake-toy-workflow-starter/scripts/check_workflow_layout.py.
3. 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.
4. 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