Configuring QIAseq analyses
Most of the analyses provided in the QIAseq Panel Analysis Assistant can be run in different ways:
From the QIAseq Panel Analysis Assistant.
- How to do this: Click Run in the QIAseq Panel Analysis Assistant wizard. See Running a QIAseq analysis for details.
- Considerations: Launching analyses using the QIAseq Panel Analysis Assistant is simple because most parameters are preconfigured.
From the Toolbox.
- How to do this: Click Find in Toolbox under More in the QIAseq Panel Analysis Assistant wizard.
- Considerations: More parameters are available for configuration than when launching using the QIAseq Panel Analysis Assistant.
From a copy.
- How to do this: Click Open Copy of Workflow under More in the QIAseq Panel Analysis Assistant wizard.
- Considerations:
- Only possible for analyses that use template workflows.
- All parameters are available for configuration.
- Needed if the analysis in the QIAseq Panel Analysis Assistant applies different parameters compared to the template workflow. Such analyses are marked using (
), see Non-standard parameters in QIAseq analyses for details.
- The workflow copy can further be adapted to better suit a specific panel/kit.
Starting the analysis from the Toolbox or using a copy also allows to:
- Use a different Reference Data Set.
- Define batch units based on metadata.
Opening and configuring a workflow copy
To open a copy of the pre-configured workflow used by an analysis, click Open Copy of Workflow under More in the QIAseq Panel Analysis Assistant wizard. The workflow copy is configured with the corresponding reference data (Reference data for QIAseq analyses) and has the same parameters as those used when running the workflow directly from the QIAseq Panel Analysis Assistant.
When opening a copy of the workflow,
- If all needed Reference Data Elements have been previously downloaded to the CLC Workbench, or, if relevant, to the CLC Server that the CLC Workbench is logged into, the copy opens in the background.
- If there are missing Reference Data Elements, a "Reference data" wizard offers to download them (figure 14.109). The download can be skipped by clicking Finish.
Figure 14.109: Download missing Reference Data Elements when opening a workflow copy. The "Download to Server" button is present because the CLC Workbench is logged into a CLC Server and the Reference Data Element is also missing from the CLC Server.
When there are missing Reference Data Elements and the download is skipped in the "Reference data" wizard (figure 14.109), the workflow fails to validate (see Validating a workflow) due to the missing data (figure 14.110). To run the workflow, either download the missing Reference Data Element or configure the workflow to use different data. See Configuring input and output elements for information on how to design workflows using reference data.
Figure 14.110: A copy of the template workflow for the "Somatic, Illumina" analysis for the DHS-001Z panel opened from the QIAseq Panel Analysis Assistant. The step to download missing reference data was skipped and thus the workflow does not validate due to the missing target regions.
See Creating and editing workflows for information about editing workflows, Basic configuration of workflow elements and The Configuration Editor view for information about changing the parameters of the tools. Once the workflow is fully configured and saved to the Navigation Area, it can be installed, see Creating a workflow installation file for details.