======================================================================== 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. .. note:: Throughout this documentation we will use *workflow* and *pipeline* interchangeably. .. This document has the following major parts: .. - *Part I:* covers details about the features and how to use module .. - *Part II:* describes the config file .. - *Part III:* explains how to make new components .. - *PartIV:* explains how to launch a pipeline Table of Contents ================= .. toctree:: :maxdepth: 5 Getting started Package Configuration file Components Pipelines Guides License Contacts .. Versions .. Indices and tables .. ================== .. * :ref:`genindex` .. * :ref:`modindex` .. * :ref:`search` .. _Ruffus: http://www.ruffus.org.uk/ .. _YAML: http://yaml.org/ .. topic:: Citation: Please cite Kronos using `this paper `_. .. topic:: Date last updated this document: 2016-07-13