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.

Workflows

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 (https://koesterlab.github.io)
dna-seq-gatk-variant-calling	DNA-seq	Johannes Köster (https://koesterlab.github.io)
accel-amplicon-trimming	Accel Amplicon	Patrik Smeds (Clinical Genomics Uppsala)
single-cell-rna-seq	Single cell RNA-seq	Johannes Köster (https://koesterlab.github.io)

Documentation

Join the team

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

Contribute

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.

Guidelines

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.