Some plugins have settings that can be configured by users. For these plugins, there are typically three different ways they can be configured:

• Global configuration: For plugins that can be configured globally, administrator-level users can change the settings for all users of the software on a particular server (see Configure plugins globally. These default settings can be overridden when setting up a Planned Run or Planned Run template, or when running the plugin manually.

  Note:

  Some plugins require configuration, and will fail unless a user first enters certain settings. For example, some plugins require that a user enter a file directory for output files.

• Planned Run configuration: Some plugins can be configured when setting up a Planned Run or Planned Run template. These options are available under Plugins in the Planned Run Workflow bar. Settings that are selected here override the global settings.

• Manual configuration: Some plugins can be configured when they are selected to run on the data from a sequencing run after the run is complete. These plugins can be configured and run from the Run Summary screen under the Plugin Summary subtab. Settings that are selected here override the global settings or any Planned Run settings.