Input and output

Besides connecting the elements together, you have to decide what the input and the output of the workflow should be. We will first look at specification of the output, which is done by right-clicking the output box of any tool and selecting Use as Workflow Output as shown in figure 8.12.

Image workflow_output
Figure 8.12: Selecting a workflow output.

You can mark several outputs this way throughout the workflow. Note that no intermediate results are saved unless they are marked as workflow output8.1.

By double-clicking the output box, you can specify how the result should be named as shown in figure 8.13.

Image workflow_output_name
Figure 8.13: Specifying naming of a workflow output.

In this dialog you can enter a name for the output result, and you can make use of two dynamic placeholders for creating this name (press Shift + F1 to get assistance):

An example of a meaningful name to a variant track could be {2} variant track as shown in figure 8.14. If your workflow input is named Sample 1, the result would be Sample 1 variant track.

Image workflowoutputvarianttrack
Figure 8.14: Providing a custom name for the result.

In addition to output, you also have to specify where the data should go into the workflow by adding an element called Workflow Input. This can be done by:

At this point you have only prepared the workflow for receiving input data, but not specified which data to use as input. To be able to do this you must first save the workflow. When this has been done, the button labeled Run is enabled which allows you to start executing the workflow. When you click on the button labeled Run you will be asked to provide the input data.

Multiple input files can be used when:

It can be useful to rename input elements when working with multiple input files, so that it is easy to discriminate between them when they are shown during workflow execution.

Note: Once the multiple input feature is used in a workflow, it is not possible to run the workflow in batch mode.

You can choose the order in which inputs will be processed by an element by right clicking on the input parameter box at the top of the element and choosing the option Order Inputs. This is most relevant for elements involved in data visualization. The feature Order Inputs is enabled when there are at least two inputs connected to the element (see figure 8.15). A small window will open, in which you can indicate the preferred order of the inputs to that element by moving them up and down in the list (figure 8.16). From this point forward, the order of the inputs is displayed on the branches connecting the inputs to elements.

Image orderinputs1
Figure 8.15: Right-click on the input parameter box to see the Order Inputs function.

Image orderinputs2
Figure 8.16: Define the inputs order for the element.

The feature Order Workflow Inputs allows you to set the order that a user will be asked for each input when they run the workflow. This option is enabled as soon as the workflow has two or more inputs (figure 8.17). Right click on empty space in the Workflow editor to start this tool. A small window will open in which the different inputs can be moved up and down to indicate the desired order (figure 8.18).

Image order_workflow_inputs1
Figure 8.17: Right click on empty space in the Workflow editor to open the Order Workflow Inputs tool.

Image order_workflow_inputs2
Figure 8.18: Define the order of the inputs for the workflow.

The example in figure 8.19 shows how to generate a track list in a workflow. Any track based on a compatible genome can be added to the same track list. This includes reference tracks as well as track results generated by elements of that workflow. In the latter case, only those for which a workflow output element has been configured can be included in a track list.

Image workflow_create_track_list
Figure 8.19: Generation of a track list including data generated within the Workflow, as well as data held in the Workbench.


Footnotes

... output8.1
When the workflow is executed, all the intermediate results are indeed saved temporarily but they are automatically deleted when the workflow is completed. If a part of the workflow fails, the intermediate results are not deleted.