Installing and configuring workflows

After a workflow is created in a CLC Workbench, an installer file can be created, as described on

Workflow installer files can be used to install the workflow onto other CLC Workbenches or onto the onto the CLC Server. When logged into the CLC Server from a Workbench as a user with administrative rights, workflows can also be installed onto the server directly from the Workbench.

When working logged into the CLC Server web interface as an administrative user, workflows can be installed by going to:

        Admin (Image preferences) | Workflows (Image workflows_16_n_p)

Click the Install Workflow button and select a workflow installer file.

Once installed, a validated (Image checkmark) or attention (Image exclamation) status icon will be shown to the left of the workflow name, as shown in figure 13.1.

Image workflow_on_server-genomics-server
Figure 13.1: The workflow named Small Variant Calling Workflow is installed on the server and has been validated. The worfklow below, named qctargetsequencing-bxwb5 is installed, but there are issues that need to be addressed.

The workflow elements with red text are ones that can be configured. Click on such an element to bring up a dialog with a listing the parameters that can be configured, as well as an overview of the locked parameters. An example is shown in figure 13.2.

Image workflow_read_mapping_serverconfig
Figure 13.2: In this example only one parameter can be configured, the rest of the parameters are locked for the user.

Open parameters can be configured, and can also be locked if desired, so that the parameter cannot be changed when executing the workflow. Locking and unlocking parameters is described further here:

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.