CGAT-showcase documentation!

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cgat-showcase contains a basic RNA-seq differential expression pipeline to illustrate how to build workflows using the cgat-core workflow management system. cgatcore allows you to quickly build both simple and complex pipelines for reproducible data analysis within a python script.

cgat-core is a set of libraries and helper functions that enable researchers to quickly design and build computational workflows for the analysis of large-scale data-analysis. Access to code is through github and documentation can be accessed here.

Used in combination with cgat-apps, we have deomonstrated the functionality of our flexible implementation using a set of well documented, easy to install and easy to use workflows, which can be found in our cgat-flow repository.

However, in this repository we have developed a toy example showing the functionality of our code. For further information on the advanced functionality of our code please refer to the cgat-flow docuemntation.

cgat-core is a user-friendly and powerful open-source workflow management system and has been continually developed and used for implemention Next Generation Sequencing (NGS) pipelines for over 10 years.

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