Adding workflow elements

First, click the Add Element (Image add_plus) button at the bottom (or use the shortcut Shift + Alt + E). This will bring up a dialog that lists the elements and tools, which can be added to a workflow (see figure 10.1).

Alternatively elements can be dragged directly from the Toolbox into the workflow. Only workflow enabled elements can be dropped in the workflow.

Image workflow_add_elements
Figure 10.1: Adding elements in the workflow.

Elements that can be selected in the dialog are mostly tools from the Toolbox. However, there are two special elements on the list: the elements that are used for input and output.

You can select more than one element in the dialog by pressing Ctrl (Image command_key_web on Mac) while selecting. Click OK when you have selected the relevant tools. You can add more later on if you wish.

You will now see the selected elements in the editor (see figure 10.2).

Image workflow_two_elements
Figure 10.2: Read mapping and variant calling added to the workflow.

Once added, you can move and rearrange the elements by dragging them with the mouse. To do this, click on part of the box containing the name of the element and then, keeping the mouse button depressed, drag the element to the desired position.

Adding to workflows

Additional elements can be added to an already existing workflow by dragging it from the navigation area into the workflow editor and joining more elements as necessary. The new workflow must be saved and validated before it can be executed. Two or more workflows can be joined by dragging and dropping one from the Navigation Area, into another that is already open in the main viewing area. The output of one must be connected to the input of the next to allow the whole workflow to run in one go.

Workflows do not need to be valid to be dragged in to the workflow editor, but they must have been updated to the current version of the workbench.