Snakemake
5.22.1

Getting started

  • Installation
  • Snakemake Tutorial
  • Short tutorial
  • Snakemake Executor Tutorials

Executing workflows

  • Command line interface
  • Cluster Execution
  • Cloud execution
  • Between workflow caching
  • Interoperability

Defining workflows

  • Writing Workflows
  • Rules
  • Configuration
  • Modularization
  • Remote files
  • Utils
  • Distribution and Reproducibility
  • Reports

API Reference

  • The Snakemake API
  • Additional utils
  • Internal API

Project Info

  • Citing and Citations
  • More Resources
    • Talks and Posters
    • External Resources
  • Frequently Asked Questions
  • Contributing
  • Credits
  • Change Log
  • License
Snakemake
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More Resources¶

Talks and Posters¶

  • Poster at ECCB 2016, The Hague, Netherlands.

  • Invited talk by Johannes Köster at the Broad Institute, Boston 2015.

  • Introduction to Snakemake. Tutorial Slides presented by Johannes Köster at the GCB 2015, Dortmund, Germany.

  • Invited talk by Johannes Köster at the DTL Focus Meeting: “NGS Production Pipelines”, Dutch Techcentre for Life Sciences, Utrecht 2014.

  • Taming Snakemake by Jeremy Leipzig, Bioinformatics software developer at Children’s Hospital of Philadelphia, 2014.

  • “Snakemake makes … snakes?” - An Introduction by Marcel Martin from SciLifeLab, Stockholm 2015

  • “Workflow Management with Snakemake” by Johannes Köster, 2015. Held at the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

External Resources¶

These resources are not part of the official documentation.

  • A number of tutorials on the subject “Tools for reproducible research”

  • Snakemake workflow used for the Kallisto paper

  • An alternative tutorial for Snakemake

  • An Emacs mode for Snakemake

  • Flexible bioinformatics pipelines with Snakemake

  • Sandwiches with Snakemake

  • A visualization of the past years of Snakemake development

  • Japanese version of the Snakemake tutorial

  • Basic and advanced french Snakemake tutorial.

  • Mini tutorial on Snakemake and Bioconda

  • Snakeparse: a utility to expose Snakemake workflow configuation via a command line interface

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