Configuring input and output elements

Configuring Workflow Input elements

Workflow Input elements and NGS Import elements are the two element types that bring data into a workflow.

At least one such element must be present in a workflow. By default, when a workflow is launched, the workflow wizard will prompt for data to be selected from the Navigation Area, or for data files to be imported on-the-fly using any compatible importer, as described in Importing data on the fly.

If desired, Workflow Input elements can be configured to restrict the options for data selection available when launching the workflow. To configure these elements, double click on them or right-click on an element name and select the Configure... option. This opens a dialog like that in figure 12.25.

Common configurations for Workflow Input elements include:

Configuring Workflow Output and Export elements

Results generated by a workflow are only saved if the relevant output channel of a workflow element is connected to a Workflow Output element or an Export element. Data sent to output channels without an Output or Export element attached are not saved.

Terminal workflow elements with output channels must have at least one Workflow Output element or Export element connected.

The naming pattern for workflow outputs and exports can be specified by configuring Workflow Output elements and Export elements respectively. To do this, double click on a Workflow Output or Export element, or right-click and select the option Configure.... Naming patterns can be configured in the Custom output name field in the configuration dialog.

The rest of this section is about configuring the Custom output name field, with a focus on the use of placeholders. This information applies to both Workflow Output elements and Export elements. Other configuration settings for Export elements are the same as for export tools, described in Export tool parameters. Placeholders available for export tools, run directly (not via a workflow) are different and are described in export tools section of the manual.

Configuring custom output names

By default, a placeholders is used to specify the name of an output or exported file, as seen in figure 12.28. Placeholders specify a type of information to include in the output name, and are a convenient way to apply a consistent naming pattern. They are replaced by the relevant information when the output is created.

The placeholders available are listed below. Hover the mouse cursor over the Custom output name field in the configuration dialog to see a tooltip containing this list. Text-based forms of the placeholders are not case specific.

You can choose any combination of the placeholders and text, including punctuation, when configuring output or export names. For example, {input}({day}-{month}-{year}), or {2} variant track as shown in figure 12.29. In the latter case, if the first workflow input was named Sample 1, the name of the output generated would be "Sample 1 variant track".

Image workflow_output_name
Figure 12.28: The names that outputs are given can configured. The default naming uses the placeholder {1}, which is a synonym for the placeholder {name}.

Image workflowoutputvarianttrack
Figure 12.29: Providing a custom name for the result.

It is also possible to save workflow outputs and exports into subfolders by using a forward slash character / at the start of the output name definition. For example the custom output name /variants/{name} refers to a folder "variants" that would lie under the location selected for storing the workflow outputs. When defining subfolders for outputs or exports, all later forward slash characters in the configuration, except the last one, will be interpreted as further levels of subfolders. For example, a name like /variants/level2/level3/myoutput would put the data item called myoutput into a folder called level3 within a folder called level2, which itself is inside a folder called variants. The variants folder would be placed under the location selected for storing the workflow outputs. If the folders specified in the configuration do not already exist, they are created.

Note: In some circumstances, outputs from workflow element output channels without a Workflow Output element or an Export element connected may be generated during a workflow run. Such intermediate results are normally deleted automatically after the workflow run completes. If a problem arises such that the workflow does not complete normally, intermediate results may not be deleted and will be in a folder named after the workflow with the word "intermediate" in its name.