Snakemake—a scalable bioinformatics workflow engine

Snakemake - a scalable bioinformatics workflow engine

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:/...

SAASFEE: Scalable Scientific Workflow Execution Engine

Across many fields of science, primary data sets like sensor read-outs, time series, and genomic sequences are analyzed by complex chains of specialized tools and scripts exchanging intermediate results in domain-specific file formats. Scientific workflow management systems (SWfMSs) support the development and execution of these tool chains by providing workflow specification languages, graphic...

Endofday: A Container Workflow Engine for Scalable, Reproducible Computation

Container technologies such as Docker [1] are transforming the way distributed systems are deployed onto cloud platforms by providing a simple mechanism for packaging and isolating an application and its dependencies from the host machine on which it is running. The same ideas and technologies can be applied to computational science applications to obtain exceptional ease of installation and re...

Workflow Database Administration Workflow Engine DocumentManagement

Workflow Process Engine Interface External Workflow Engines

We introduce the ActivityFlow speciication language for in-cremental speciication and exible coordination of workkow activities. The most interesting features of the ActivityFlow speciication language include (1) a collection of speciication mechanisms, which provides a workkow designer with a uniform workkow speciication interface to describe diierent types (i.e., ad-hoc, administrative, or pr...