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File Actions

File Actions allow one to automate the execution of actions when new files are added to a project. An action consists of the following:

  • A glob pattern used for matching against new files. The action will only execute if the glob pattern matches against the new file name.
  • A Workflow to execute against the new file(s).

Access Control

To create File Actions in a project, you must have Rules Admin>Access privileges. To grant privileges, see Access Control.

Creating a File Action

When adding an Action, you will follow a path to set up the File Action parameters. As you complete the steps, you'll advance to the next section. You can use the Next or Back buttons to navigate within the path.

  1. Navigate to the File Actions web console and click the Add Action button in the top header.

  2. On the Settings page that opens (see image below), provide:

    • A name for the Action.
    • A path for the work product of the Action (optional).
    • A notification email on Action completion success and/or failures (optional). In the example shown, a File Action to process Caris test files is created. Specify Name
  3. Select the CWL Workflow tool that the action will run. In the example shown, we used the search box above the table to filter our results and find the Caris tool. Select CWL File

  4. Provide the glob patterns to use for matching files. In the example shown a file uploaded to caris/sn-0045.tar.gz would match and start the workflow with the sn-0045.tar.gz file as it's only file input. Enter File Pattern

  5. Provide values for any string inputs. File inputs will automatically be populated with the newly uploaded file. For string inputs, one can use {{name}} to substitute in the name of newly uploaded or any static string the workflow requires. In the example shown, the workflow requires the genome reference as a string so that's provided. Select CWL File

  6. Review the Action settings and click Next to create the action. Review

  7. The newly created action is now visible in the list of the project's File Actions. Review


Last update: 2021-10-04