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.
| Workflow | Domain | Authors |
|---|---|---|
| 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) |
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
cookiecutter gh:snakemake-workflows/cookiecutter-snakemake-workflow. - 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.