Analysis Workflows

Analysis workflows are packaged templates of BaseSpace Sequence Hub Apps with predefined settings and QC thresholds to support automation of running analyses. Use an analysis workflow to automatically launch the same app configurations on different biosamples in the project.

When you assign an analysis workflow using a biosample workflow file, the workflow status is listed as Pending. After data are received and conditional dependencies are met, the analysis is launched and the status is listed as Running.

Create an Analysis Workflow

For information about creating an Analysis Workflow for an existing app, using your own settings or QC thresholds with an existing BaseSpace Sequence Hub app, see the developer documentation at

Modify an Analysis Workflow

Analysis Workflows can be modified by their owners or members of the workgroup in which the workflow was created. If you need to modify a workflow, Illumina recommends creating a new workflow and adding a version number to the workflow name.

Schedule Analysis Workflow to Automatically Launch

  1. Upload a Biosample Manifest with analysis workflows set for one or more biosamples. See Biosample Workflow.

  2. Sequence data for the biosample.

  3. BaseSpace Sequence Hub checks that dependencies are met, collects data sets associated with the biosample, and launches the analysis.

BaseSpace Sequence Hub excludes datasets that have been QC Failed or are linked to QC failed libraries, pools, or lanes.

Cancel an Analysis

  1. Select one or more analyses that are Running or Pending.

  2. Select the Status drop-down arrow, point to Cancel, and then select Analysis.

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