Documentation of the Snakemake-Workflows project
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The Snakemake-Workflows project

The Snakemake-workflows project is a joint effort to create workflows for common use cases of the Snakemake workflow management system.


A list of all available workflows that are currently in development can be found here.

Approved workflows

The following workflows have undergone a strict review and quality control process and are ready for production. They can be considered as best practice examples.

Workflow Domain Authors
rna-seq-star-deseq2 RNA-seq Johannes Köster (
dna-seq-gatk-variant-calling DNA-seq Johannes Köster (
accel-amplicon-trimming Accel Amplicon Patrik Smeds (Clinical Genomics Uppsala)
single-cell-rna-seq Single cell RNA-seq Johannes Köster (


Join the team

Once the initiators have agreed on the procedure, it will be possible to join the team here.


Contributing is easy:

  1. Join the team
  2. Create a new repository for your workflow
  3. Ensure that your workflow meets our guidelines.
  4. Request a review here.


  1. A workflow repository shall consist of one Snakemake workflow.
  2. The structure of the workflow should follow our template. You can create a new workflow with cookiecutter via cookiecutter gh:snakemake-workflows/cookiecutter-snakemake-workflow.
  3. Whenever possible, Snakemake wrappers should be used.
  4. The workflow should be configurable via a well documented YAML-based configuration file and (when necessary) a sample and a unit sheet (see here for an example).
  5. The workflow has to define an (integration-style) test case that is configured via the .travis.yml file in the skeleton.