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snakemake-workflows

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Documentation of the Snakemake-Workflows project

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)
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)

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 from it by clicking the Use this template button on the template repositories page. And just follow the TODOs from there.
  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.
  6. For inclusion in the snakemake workflow catalog, further follow the catalog inclusion requirements.

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