Building and Documenting Workflows with Python-Based Snakemake

Köster, Johannes; Rahmann, Sven

doi:10.4230/OASIcs.GCB.2012.49

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Building and Documenting Workflows with Python-Based Snakemake

Authors Johannes Köster, Sven Rahmann

Part of: Volume: German Conference on Bioinformatics 2012 (GCB 2012)
Part of: Series: Open Access Series in Informatics (OASIcs)
License: Creative Commons Attribution-NoDerivs 3.0 Unported license
Publication Date: 2012-09-13

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OASIcs.GCB.2012.49.pdf

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Document Identifiers

DOI: 10.4230/OASIcs.GCB.2012.49
URN: urn:nbn:de:0030-drops-37179

Subject Classification

Keywords

workflow engine
dependency graph
knapsack problem
Python
high-throughput sequencing
next-generation sequencing

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Abstract

Snakemake is a novel workflow engine with a simple Python-derived workflow definition language and an optimizing execution environment. It is the first system that supports multiple named wildcards (or variables) in input and output filenames of each rule definition. It also allows to write human-readable workflows that document themselves. We have found Snakemake especially useful for building high-throughput sequencing data analysis pipelines and present examples from this area. Snakemake exemplifies a generic way to implement a domain specific language in python, without writing a full parser or introducing syntactical overhead by overloading language features.

Cite As Get BibTex

Johannes Köster and Sven Rahmann. Building and Documenting Workflows with Python-Based Snakemake. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 49-56, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012) https://doi.org/10.4230/OASIcs.GCB.2012.49

Author Details

Johannes Köster

Sven Rahmann

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