Installing and configuring workflows

Workflows installed on a CLC Server are available to launch from the Toolbox of CLC Workbench clients or using the CLC Server Command Line Tools.

Workflows can be installed on the CLC Server using a workflow installer file, or installed as the final step when creating a workflow installer in a CLC Workbench. To install a workflow, you must have the relevant permissions (Controlling access to the server, server tasks and external data).

Creating workflow installer files is described at:

When logged into the web administrative interface as a user with rights to administer workflows, workflows can be installed by going to:

        Extensions (Image extensions_16) | Manage Workflows (Image workflows_16)

Click on the Install Workflow button and select a workflow installer file to install it.

After installation a green check mark (Image checkmark) is shown to the left of the workflow name when the workflow is ready to use. If there is an issue that needs to be attended to, a red exclamation mark (Image exclamation) is shown (figure 9.1).

If the workflow installer includes bundled reference data, that data will be stored in a subfolder of a folder called Plugin_data in the first available file system location. The subfolder name will include the name and version of the workflow.

Image workflow_on_server-genomics-server
Figure 9.3: The workflow called Prepare Raw Data with Updated Names is ready to use. There is a problem with the other workflow, as indicated by the red exclamation mark.

Click on the name of the workflow to reveal a pictorial representation of it. Further details about any problems are presented in this view (figure 9.2) .

Image workflow_on_server-expanded-genomics-server
Figure 9.4: A workflow with an issue is visible. The Create Sample Report element needs to be updated as the version of the tool on the CLC Server is different to the one that the workflow was configured to use.

Workflow elements with red text can be configured. Clicking on a configurable element opens a dialog where values of open parameters can be changed and a list of the locked parameters is provided (figure 9.3).

Image workflow_read_mapping_serverconfig
Figure 9.2: Configuring a workflow element. One parameter in this element can be configured. The rest were locked in the workflow before the workflow installer was created.

Open parameters can be locked, if desired. When a parameter is locked, its value cannot be changed when launching the workflow. Locking and unlocking parameters is described further at

If changes to the parameter settings of an installed workflow are made, the timestamp of the most recent change and the name of the administrator who made those changes are reported at the top of the workflow configuration view.

Further information about updating workflows is provided in Updating workflows.