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.
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.
|rna-seq-star-deseq2||RNA-seq||Johannes Köster (https://koesterlab.github.io)|
|rna-seq-kallisto-sleuth||RNA-seq||Johannes Köster (https://koesterlab.github.io)|
|dna-seq-gatk-variant-calling||DNA-seq||Johannes Köster (https://koesterlab.github.io)|
|dna-seq-varlociraptor||DNA-seq||Johannes Köster, Felix Mölder (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)|
|single-cell-drop-seq||Single cell RNA-seq||Patrick Roelli (TU Munich, Swiss Institute of Bioinformatics)|
Join the team
Once the initiators have agreed on the procedure, it will be possible to join the team here.
Contributing is easy:
- Join the team
- Create a new repository for your workflow
- Ensure that your workflow meets our guidelines.
- Request a review here.
- A workflow repository shall consist of one Snakemake workflow.
- The structure of the workflow should follow our template. You can create a new workflow with cookiecutter via
- Whenever possible, Snakemake wrappers should be used.
- 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).
- The workflow has to define an (integration-style) test case that is configured via the
.travis.ymlfile in the skeleton.