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 9.12.

Image workflow_output
Figure 9.12: 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 output9.1.

By double-clicking the output box, you can specify how the result should be named as shown in figure 9.13.

Image workflow_output_name
Figure 9.13: 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 9.14. If your workflow input is named Sample 1, the result would be Sample 1 variant track.

Image workflowoutputvarianttrack
Figure 9.14: 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:

Please note that once the multiple input feature is used in a workflow, it is not possible to run the workflow in batch mode. Please also note that the input elements can be renamed, which is useful if you want to be able to discriminate the elements in the process description shown during workflow execution.

The example in figure 9.15 shows how to generate a track list in a workflow. It is possible to include reference tracks and also tracks from any step, or multiple steps within the workflow as long as output Read Tracks are defined and linked to.

Image workflow_create_track_list
Figure 9.15: Generation of a track list including data generated within the Workflow, as well as data held in the Workbench.


... output9.1
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.