Snakemake specifications

Information


Unique identifier OMICS_02299
Name Snakemake
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements BWA, SAMtools, BCFtools, Graphviz, PyYAML, Docutils
Maintained Yes

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Maintainer


  • person_outline Johannes K√∂ster <>

Publication for Snakemake

Snakemake institution(s)
Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and Paediatric Oncology, University Childrens Hospital, Essen, Germany

Snakemake reviews

 (2)
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Samuel Lampa

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Desktop
A top-quality software that is really helpful for low- to medium complexity workflows, especially where you might want to re-generate certain outputs based on updated inputs.

For really complex workflows, such as when involving multiple nested parameter sweeps and/or cross-validation constructs implemented in the workflow layer, it can get a bit complicated to figure out how to write that, and something more dataflow-like like NextFlow might be preferrable in such cases.

Fabien Pichon

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A useful pipeline generator in python that allows to create modules (rules) for each step. A little bit confusing at the beginning if one doesn't know make but very powerful at the end. An important point : Snakemake allows graphics workflow output.