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DOI: 10.4230/OASIcs.GCB.2012.49
URN: urn:nbn:de:0030-drops-37179
URL: http://drops.dagstuhl.de/opus/volltexte/2012/3717/
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Köster, Johannes ; Rahmann, Sven

Building and Documenting Workflows with Python-Based Snakemake

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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.

BibTeX - Entry

@InProceedings{kster_et_al:OASIcs:2012:3717,
  author =	{Johannes K{\"o}ster and Sven Rahmann},
  title =	{{Building and Documenting Workflows with Python-Based Snakemake}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{49--56},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{Sebastian B{\"o}cker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2012/3717},
  URN =		{urn:nbn:de:0030-drops-37179},
  doi =		{http://dx.doi.org/10.4230/OASIcs.GCB.2012.49},
  annote =	{Keywords: workflow engine, dependency graph, knapsack problem, Python, high-throughput sequencing, next-generation sequencing}
}

Keywords: workflow engine, dependency graph, knapsack problem, Python, high-throughput sequencing, next-generation sequencing
Seminar: German Conference on Bioinformatics 2012
Issue Date: 2012
Date of publication: 13.09.2012


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