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Bioinformatics. 2012 Oct 1;28(19):2520-2. Epub 2012 Aug 20.

Snakemake--a scalable bioinformatics workflow engine.

Author information

1
Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and Paediatric Oncology, University Childrens Hospital, 45147 Essen, Germany. johannes.koester@uni-due.de

Abstract

SUMMARY:

Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

AVAILABILITY:

http://snakemake.googlecode.com.

CONTACT:

johannes.koester@uni-due.de.

PMID:
22908215
DOI:
10.1093/bioinformatics/bts480
[Indexed for MEDLINE]

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