The CLC Genomics Workbench provides a framework for creating, distributing, installing and running workflows. Workflows created in the Workbench can also be installed on a CLC Genomics Server.

A work flow consists of a series of tools where the output of one tool is connected as the input to another tool. In this way you can set up a workflow to go through for example read mapping, using the mapped reads as input for variant detection, and perform some filtering of the variant track. Once the workflow is set up, it can be installed (either in your own Workbench or on a Server or sent to a colleague) and you can then analyze a lot of samples using the same standard pipeline using the same reference data and parameters.

This chapter will first explain how to create a new workflow, and next go into details about the installation and execution of a workflow. For information about installing a workflow on the CLC Genomics Server, please see the user manual at