Snakemake
stable

Getting started

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

Executing workflows

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

Defining workflows

  • Writing Workflows
  • Snakefiles and Rules
  • Configuration
  • Modularization
  • Remote files
  • Utils
  • Distribution and Reproducibility
  • Reports
  • Automatically generating unit tests
  • Integrating foreign workflow management systems

Project Info

  • Citing and Citations
  • More Resources
    • Talks and Posters
    • External Resources
  • Frequently Asked Questions
  • Contributing
  • Credits
  • Changelog
  • License
Snakemake
  • Docs »
  • More Resources
  • Edit on GitHub

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

Next Previous

© Copyright 2014-2023, Johannes Koester Revision 1c9ea65d.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: stable
Versions
master
latest
stable
v7.20.0
v7.19.1
v7.19.0
v7.18.2.1
v7.18.2
v7.18.1
v7.18.0
v7.17.2
v7.17.1
v7.17.0
v7.16.2
v7.16.1
v7.16.0
v7.15.2
v7.15.1
v7.15.0
v7.14.2
v7.14.1
v7.14.0
v7.13.0
v7.12.1
v7.12.0
v7.11.0
v7.10.0
v7.9.0
v7.8.5
v7.8.4
v7.8.3
v7.8.2
v7.8.1
v7.8.0
v7.7.0
v7.6.2
v7.6.1
v7.6.0
v7.5.0
v7.4.0
v7.3.8
v7.3.7
v7.3.6
v7.3.5
v7.3.4
v7.3.3
v7.3.2
v7.3.1
v7.3.0
v7.2.1
v7.2.0
v7.1.1
v7.1.0
v7.0.4
v7.0.3
v7.0.2
v7.0.1
v7.0.0
v6.15.5
v6.15.4
v6.15.3
v6.15.2
v6.15.1
v6.15.0
v6.14.0
v6.13.1
v6.13.0
v6.12.3
v6.12.2
v6.12.1
v6.12.0
v6.11.1
v6.11.0
v6.10.0
v6.9.1
v6.9.0
v6.8.2
v6.8.1
v6.8.0
v6.7.0
v6.6.1
v6.6.0
v6.5.5
v6.5.4
v6.5.3
v6.5.2
v6.5.1
v6.5.0
v6.4.1
v6.4.0
v6.3.0
v6.2.1
v6.2.0
v6.1.2
v6.1.1
v6.1.0
v6.0.5
v6.0.4
v6.0.3
v6.0.2
v6.0.1
v6.0.0
v5.32.2
v5.32.1
v5.32.0
v5.31.1
v5.31.0
v5.30.2
v5.30.1
v5.30.0
v5.29.0
v5.28.0
v5.27.4
v5.27.3
v5.27.2
v5.27.1
v5.27.0
v5.26.1
v5.26.0
v5.25.0
v5.24.2
v5.24.1
v5.24.0
v5.23.0
v5.22.1
v5.22.0
v5.21.0
v5.20.1
v5.20.0
v5.19.3
v5.19.2
v5.19.1
v5.19.0
v5.18.1
v5.18.0
v5.17.0
v5.16.0
v5.15.0
v5.14.0
v5.13.0
v5.12.3
v5.12.2
v5.12.1
v5.12.0
v5.11.2
v5.11.1
v5.11.0
v5.10.0
v5.9.1
v5.9.0
v5.8.2
v5.8.1
v5.8.0
v5.7.4
v5.7.3
v5.7.2
v5.7.1
v5.7.0
v5.6.0
v5.5.4
v5.5.3
v5.5.2
v5.5.1
v5.5.0
v5.4.5
v5.4.4
v5.4.3
v5.4.2
v5.4.1
v5.4.0
v5.3.1
v5.3.0
v5.2.4
v5.2.3
v5.2.2
v5.2.1
v5.2.0
v5.1.5
v5.1.4
v5.1.3
v5.1.2
v5.1.1
v5.0.0
v4.8.1
v4.8.0
v4.7.0
v4.6.0
v4.5.1
v4.5.0
v4.3.0
v4.2.0
v4.1.0
v4.0.0
v3.13.3
v3.13.2
v3.13.1
v3.13.0
v3.12.0
v3.11.2
v3.11.1
v3.11.0
v3.10.2
v3.10.1
v3.10.0
v3.9.1
v3.9.0
v3.7.1
Downloads
On Read the Docs
Project Home
Builds

Free document hosting provided by Read the Docs.