Launching workflows individually and in batches

Workflows can be launched:

From under the Toolbox menu by double clicking on an installed workflow.
From a Workflow Editor by clicking on the Run Workflow button at the bottom of the Workflow Editor.
Double-clicking on a saved workflow design in the Navigation Area opens it in the Workflow Editor. Installed workflows can be opened in the Workflow Editor by selecting them in the Toolbox in the bottom, left side of the CLC Genomics Workbench, right-clicking and selecting the option Open Copy of Workflow.

When a workflow is launched, a wizard is opened. Stepping through this wizard, configurable parameters can be reviewed and changed as needed, and the locations that outputs should be saved under can be specified. Where input elements are configured with a role, the workflow launch wizard will require you to select (and potentially download) the relevant reference data.

If you are connected to a CLC Genomics Server, the wizard will include the option to run the workflow locally on the Workbench or on the server.

If the workflow is not properly configured, you will see that in the dialog when the workflow is launched^12.2.

One of the outputs that can be generated by a workflow run is a workflow result metadata table. This metadata table contains a row for each of the outputs generated by the workflow, and each row is associated with the relevant data objects. Workflow result metadata tables are particularly useful for navigating to results of workflows run in batch mode, and are described further in Workflow outputs and workflow result metadata tables.

Some aspects of launching workflows are different to launching tools, and can be more efficient and flexible, including:

Data can be imported as the first action taken when launching a workflow, saving doing this as a separate activity.
Batch units can be defined using metadata, or, for simple workflows, based on the organization of the data in the Navigation Area. For individual tools, batch units can only be defined based on data organization.
Metadata can be read from an Excel file as an integrated part of launching workflows in batch mode. This can save much hands-on work.
Data used for multiple workflow inputs can be changed for each batch run. For example, a single workflow could be launched in batch mode, where reads from some samples would be mapped to a particular reference, but reads from other samples would be mapped to other references.
As well as running whole workflows in batches, workflows can be designed such that just parts will run in batches. Results from those batched sections can then follow different downstream paths in the workflow, if desired.

The following aspects relating to launching workflows are covered in this section:

Importing data as part of a workflow run: Importing data on the fly
Workflow result metadata tables: Workflow outputs and workflow result metadata tables
Launching workflows in batch mode: Running workflows in batch mode
Launching workflows with more than one input that should change per batch run: Batching workflows with more than one input changing per run.
Running sections of a workflow in batches: Batching part of a workflow

Footnotes

... launched ^12.2: If the workflow uses a tool that is part of a plugin, a missing plugin can also be the reason why the workflow is not enabled. A workflow can also become outdated because the underlying tools have changed since the workflow was created (see Workflow identification and versioning)

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Launching workflows individually and in batches

Footnotes