The CLC Cancer Research 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 workflow consists of a series of connected tools where the output of one tool is used as input for another tool. In this way you create a workflow that for example makes a read mapping, uses the mapped reads as input for variant detection, and performs 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 it can be sent to a colleague). In that way it becomes possible to analyze lots of samples using the same standard pipeline, the same reference data and the same 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

Note that the examples below are using tools from the CLC Genomics Workbench that are not available in the CLC Cancer Research Workbench. But the principles and workflow framework can be used in the same way with tools from CLC Cancer Research Workbench.