Providing alternative CNV controls

This section describes how to create and modify a copy of a template workflow configured with QIAGEN CNV control reference data so that it can be used with alternative CNV controls.

  1. Find the template workflow in the Toolbox, right-click on it, and select Open Copy of Workflow.
  2. Locate and expand the "CNV Detection" group. Searching for cnv detection using the Find palette in the Side Panel can help locate the group.

  3. Delete the connections from Branch on XY and Remove Targets on XY to Copy Number Variant Detection (Targeted) (figure 12.6).

    Image cnv_controls_1
    Figure 12.6: The "CNV Detection" group in a template workflow that is configured with QIAGEN CNV control reference data.

  4. Drag the input connect from Analysis Options (CNV) and move it to the "Target regions track" input channel of Copy Number Variant Detection (Targeted) (figure 12.6).
  5. Delete the following workflow elements:
    • Analysis Options (CNV)
    • Prepare CNV Target Regions
    • Branch on XY
    • Remove Targets on XY
    • Analysis Options (CNV controls)
    • Check CNV Controls for XY
    • Select XY Controls

    To delete an element, first select it and then use one of the following options:

    • Press the Delete key on the keyboard.
    • Click on Delete (Image delete_document_2_16_n_p) in the top Toolbar.
    • Right-click on the element and choose Delete Selected (Image blue_delete_16_h_p).

    The group content should resemble that in figure 12.7.

    Image cnv_controls_2
    Figure 12.7: The "CNV Detection" group after removing elements.

  6. Double-click on the "CNV controls" Workflow Input element. In the "Configure CNV controls" dialog that opens (figure 12.8):

    Image configure_cnv_controls
    Figure 12.8: Configuring the "CNV controls" workflow element.

    1. Click on the  (Image browse_16_n_p) button.

    2. In the "Select Workflow Input" dialog, remove the preconfigured QIAGEN CNV control reference data by selecting them and clicking on the arrow that points to the left (Image blue_arrow_left_16_d_p) (figure 12.9).

      Click on OK.

      Image remove_cnv_control_inputs
      Figure 12.9: Removing the preconfigured QIAGEN CNV control reference data elements.

    3. Delete the preconfigured cnv_control_coverage text in the "Workflow role" field (figure 12.8).
    4. Click on OK to save and close the dialog.
  7. Save the workflow in the Navigation Area by clicking on Save (Image save_blue_16_n_p) in the top Toolbar.

When running the modified workflow copy, the alternative CNV controls can be selected in the Select CNV controls wizard step.