CGAT-core documentation!
CGAT-core is a workflow management system that allows users to quickly and reproducibly build scalable data analysis pipelines. CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.
Used in combination with CGAT-apps, we have deomonstrated the functionality of our flexible workflow management system using a simple RNA-seq pipeline in cgat-showcase.
CGAT-core is open-sourced, powerful and user-friendly, and has been continually developed as a Next Generation Sequencing (NGS) workflow management system over the past 10 years.
For more advanced examples of cgatcore utilities please refer to our cgat-flow repository, however please be aware that this is in constant development and has many software dependancies.
Citation
Our workflow management system is published in F1000 Research:
Cribbs AP, Luna-Valero S, George C et al. CGAT-core: a python framework for building scalable, reproducible computational biology workflows [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2019, 8:377 (https://doi.org/10.12688/f1000research.18674.1)
Support
Examples
- cgat-showcase
This is a toy example of how to develop a simple workflow. Please refer to the github page and the documentation.
- cgat-flow
As an example of the flexibility and functionality of CGAT-core, we have developed a set of fully tested production pipelines for automating the analysis of our NGS data. Please refer to the github page for information on how to install and use our code.
- Single cell RNA-seq
The cribbs lab use CGAT-core to develop pseudoalignment pipelines for single cell dropseq methods The sansom lab use the CGAT-core workflow engine to develop single cell sequencing analysis workflows.
Selected publications using CGAT-core
CGAT-core has been developed over the past 10 years and as such has been used in many previously published articles
For a non-comprehensive list of citations please see our :citing and Citing and Citations