Skip to content

Add a Tool

You select a tool from the Tools Registry to create a workflow in the PHC web console. A tool is a wrapper for PHC tasks and other operations and uses the Common Workflow Language (CWL) to describe the workflow. The tool follows the schema for the Global Alliance for Genomics and Health (GA4GH) Tool Registry API and uses the extension .cwl. To find examples of CWL workflows, see Dockstore, a registry of Docker based tools and workflows for the sciences defined in CWL or WDL.

  1. On the PHC side menu, click Automation and Tools Registry.
  2. On the Tools Registry screen, click Add Tool. Add Tool
  3. On the Add Tool screen, enter a useful name and description.
  4. In the Labels field, enter a general term or terms to classify the tool and create a label. Enter multiple terms as a comma delimited list, such as "bam,samtools,read depth". You can use these labels to filter tools on the Tools Registry page.
  5. In the Class field, choose Workflow or Jupyter Notebook depending on your tool type.
  6. From the Access menu, choose who can use your tool:
    • Private - Only the creator of the tool can access this tool.
    • Account - Anyone that belongs to your PHC account can access this tool. This typically limits use to your institution or company.
    • Precision Health Cloud - Anyone with a PHC account can access the tool.
    • Public - Anyone with a PHC account can access the tool and future access may extend to people without a PHC account.
  7. Click Next. Add Tool Next
  8. On the Version screen, in the Version field, enter a string, for example 1.0 or alpha.
  9. Click Select File and navigate to the .cwl file that contains the workflow or an .ipynb file for Jupyter Notebooks and click Open.
  10. Click Next. Add Tool Version
  11. On the Confirm screen, verify your configuration is correct and click Add.
  12. On the Tools Registry screen, confirm the tool appears.
  13. PHC runs a workflow validation test on uploaded .cwl files. To see the results of the test, mouse over the tool to reveal icons.

    • If the Run Icon Run Workflow icon is present, as shown in the example, the tool file passed the validation test and is ready to attach to a workflow.
    • If the Tool Error Message icon is present, the tool file failed the validation test. Click the icon to display error message information.

    Mouseover

Success

You have created a tool. To attach the tool to a workflow, complete the Add a Workflow procedure.


Last update: 2021-06-25