Workflows

Workflows contain tools linked together, making up an analysis pipeline.

Data from CLC Data Locations can be selected as input, as can raw data in supported standard formats. Results can be saved to CLC locations for viewing and downstream analysis, or exported to standard formats and saved to a location of your choice.

The flow of data through a workflow can be defined in various ways, making it simple to execute complex analyses consistently. Launching workflows in Batch mode, the same analysis is run on many samples using a single launch action.

Workflows are created and customized using the Workflow Editor (figure 13.1). Workflows can be saved and re-opened, just like data elements. You can run workflows from the Workflow Editor, or install them and run them from under the Installed Workflows folder under the Workflows menu (see Creating a workflow installation file).

Template workflows are pre-installed in the CLC Main Workbench, and can be referred to as examples, or copied and edited. This is described further in Template workflows.

Image opened_copy_of_workflow
Figure 13.1: A workflow open in the Workflow Editor. Workflows consist of connected tools, where the output of one tool is used as input for another tool.

Examples in this chapter use tools from the CLC Genomics Workbench. Some of these are not available in the CLC Main Workbench. However, the principles described apply equally to tools in CLC Main Workbench.


Subsections