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Kronos: A workflow assembler for cancer genome analytics and informatics
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``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