Basic configuration of workflow elements

Workflow elements can be renamed, and options within the elements can be customized, affecting what is seen when editing the workflow, what is seen when launching the workflow, and the settings used by default when the workflow is run.

Renaming workflow elements

Renaming workflow elements can aid understanding of a workflow design, especially when there are multiple elements for the same tool. Updated element names are reflected in the workflow launch wizard.

To rename an element, right click on the element name and choose the option "Rename...", or select the element in the Workflow Editor and press the F2 key.

The Find functionality in the side panel finds elements based the new name.

Both the new name and the original, default name of elements are provided in the Workflow Configuration view (figure 14.35). Terms in the new name or the original, default name can be used in the Filter Elements functionality of this view to find settings for configurable elements. This view is described in The Configuration Editor view.

Note: The Workflow Configuration view can be opened linked to the Workflow view. Linked views are described further in the View Area section.

Image workflow_element_names_compared
Figure 14.35: A workflow before (left) and after (right) the Map Reads to Reference element was renamed. In the linked Workflow Configuration view at the bottom right, both the original and updated element names are listed.

Configuring options in workflow elements

Configuring options can be done in a workflow element's configuration dialog by:

Options can also be edited in the Workflow Configuration view (figure 14.35).

Workflow element customization can include:

  1. Specifying which values can be changed when launching the workflow

    Beside each option is a lock symbol. Values of unlocked (Image lockopen_16_n_p) options can be changed when launching the workflow. Values of locked (Image lockclosed_16_n_p) options cannot be changed when launching the workflow.

    Click on a lock icon to change it from locked (Image lockclosed_16_n_p) to unlocked (Image lockopen_16_n_p), or vice versa.

    Image workflow_lock_unlock
    Figure 14.36: The Workflow view (top) and Workflow Configuration view (bottom) have been opened as linked views. The Map Reads to Reference element has been opened for configuration in the Workflow view and the Masking mode and Masking track options have been unlocked. They will correspondingly appear unlocked in the Workflow Configuration view after the Finish button is clicked.

    The values of all locked settings can been seen in the workflow launch wizard, but they are not presented by default (figure 14.37).

    Image workflow_wizard_locked_params
    Figure 14.37: A workflow launch wizard step showing the configurable (unlocked) options at the top, with a heading for the locked settings (top). Clicking on the Locked Settings heading reveals a list of the locked options and their values (bottom)

  2. Changing default values

    When elements are added to a workflow, the default values assigned to options are the same as the defaults for the corresponding tool from the Toolbox. Values for options can be updated in the workflow design. When this is done, the new values become the defaults used when the workflow is run.

  3. Changing option names

    When an option name is changed, the new name is used in the workflow launch wizard.

    Renaming options can be useful when only a few options can be configured when launching the workflow and their default names are quite generic.

    Click on the edit icon (Image pencil_16_n_p) beside an option to edit the name (figure 14.38).

    Image workflow_update_parameter_name
    Figure 14.38: An option originally called "Match score" has been renamed "Score for each match position" in the element configuration dialog. It has also been unlocked so the value for this option will be configurable when launching the workflow.

    Note: Clicking on the Reset button in a workflow element configuration dialog will reset all changes in that particular configuration step to the defaults, including any updated option names.