Snake

An example of a reproducible workflow with Snakemake

This is my first experience with Snakemake. See ./Snakefile for the workflow. Run bash make.sh to reproduce everything.

• The Final Report

Snakemake

I have tried GNU Make for my work to enhance reproducibility and automation but got stuck with Chinese character issues on GNU Make built for Windows. So I tried Snakemake and it looks pretty good! It is based on Python so fewer cross-platform issues should arise. It can generate a DAG for visualizing dependencies between defined workflows, which is pretty cool!

Resources

Quick Start

• Snakemake Website
• A YouTube demo of Snakemake

Docs I find useful

• Tutorial
  • Config
  • Logging
  • The script tag
  • Sub-workflows
• Recommended directory structure
• A not-so-minor bug