Kronos: A workflow assembler for cancer genome analytics and informatics

Kronos is a highly flexible Python-based software tool that mainly enables bioinformatics developers, i.e. bioinformaticians who develop workflows for analyzing genomic data, to quickly make a workflow. It uses Ruffus as the underlying workflow management system and adds a level of abstraction on top of it, which significantly reduces programming overhead for workflow development and provides a mechanism to represent a workflow by a top level YAML configuration file.

Each resulting workflow is portable, can run either locally or on a cluster, parallelizes tasks automatically, and logs all runtime events. The workflows are also highly modular and can be easily updated by editing their corresponding configuration files.

Kronos is free and open source under the MIT license and has a Docker image too. Although we have developed it with bioinformaticians in mind, Kronos can be used in any area where a workflow is required to run a series of tasks on a given set of input data.


Throughout this documentation we will use workflow and pipeline interchangeably.

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Please cite Kronos using this paper.

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