Snakemake--a scalable bioinformatics workflow engine

Bioinformatics. 2012 Oct 1;28(19):2520-2. doi: 10.1093/bioinformatics/bts480. Epub 2012 Aug 20.


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.



MeSH terms

  • Computational Biology / methods*
  • Electronic Data Processing
  • Programming Languages
  • Software*
  • Workflow*