Copy and edit an existing analysis workflow

You can copy and edit an existing analysis workflow to save time on analysis in Ion Reporter™ Software. This is the recommended way to create a user-defined analysis workflow.

Use a predefined analysis workflow or a user-defined analysis workflow to start with an optimized set of parameters.

When you create a user-defined analysis workflow, you can change details such as:

  • variant annotation filters

  • final report settings

  • analysis plugins

  • parameter settings

You can copy predefined analysis workflows and user-defined analysis workflows from the current software and from previous versions of the software. When you copy analysis workflows from an earlier version of the software, you must use target regions files, hotspots files, and fusion panel files from the same version of the software. You can view the analysis workflow version in the Details pane. For more information, see View analysis workflow details.

This procedure is typically used to create or edit the parameters of the analysis workflow for an expansion panel that is used with user-defined Ion AmpliSeq™ and Ion AmpliSeq™ HD research panels. Edits are made to an analysis workflow for the pre-existing research panel. This procedure is also used to edit the settings for a ready-to-use Ion AmpliSeq™ and Ion AmpliSeq™ HD research panel.

  1. In the Workflows tab, click Overview.
  2. In the Workflows table, click the row for the analysis workflow that you want to copy, then click  (Actions)Copy.

    The workflow bar opens to the Research Application step.

    When you copy an analysis workflow, some settings and fields are defined by the analysis workflow and remain selected.

  3. In the Research Application step, ensure the research application and sample group, then click Next.
  4. In the Reference step, ensure that the required files are selected, then click Next.
  5. In the Annotation step, ensure that one annotation set is selected, then ensure or select a MyVariants database associated with the analysis workflow, then click Next.
  6. In the Filters step, ensure or select a filter chain, then click Next.
  7. In the Copy Number step, ensure or select a copy number baseline, then click Next.
  8. In the Exon Tile Fusion step, for analysis workflows for use with assays that include RNA Exon Tiling, ensure that the appropriate Exon Tile Fusion Baseline for the analysis workflow is selected, then click Next.
  9. In the Plugins step, ensure or select plugins, then click Next.
  10. In the Final Report step, ensure or select the final report template, then click Next.
  11. In the Parameters step, ensure or edit parameters, then click Next.
  12. In the Confirm step, name the analysis workflow, enter an optional description, then click Confirm and Save Workflow.

To view the copied analysis workflow, click the Workflows tab, then click Overview, and search for the analysis workflow name then find the custom analysis workflow listed in the Workflows table.