The cgatcore library

Using cgatcore pipelines.

Motivation #

CGAT-core is a workflow management system that allows users to build data analysis pipelines.

The cgatcore python package provides a set of libraries and helper functions that enable researchers to design and build computational workflows for large-scale data analysis workflows.

In-depth documentation about cgatcore is available on ReadTheDocs →.

In this page, we provide advice for setting up the cgatcore workflow management system on the WIMM CCB cluster.

Setup #

On the CCB cluster, create the file ~/.cgat.yml and add the following lines in it.

cluster:
    queue_manager: slurm
    queue: batch
tmpdir: /tmp

First, the section cluster defines the program acting as queue manager and the name of the queue to which jobs will be submitted using the DRMAA library.

The field tmpdir defines the temporary directory used by cgatcore for writing temporary files during the execution of workflows.