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:

        Configuration (Image configuration_16) | Workflows (Image workflows_16)

Click on 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 8.1.

Image workflow_on_server-genomics-server
Figure 8.1: 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, as indicated by the red exclamation mark.

If the workflow installer included bundled reference data, those data elements will be installed into 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.

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 8.2.

Image workflow_read_mapping_serverconfig
Figure 8.2: 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.