This article includes step-by-step instructions to run the Genomics Screening workflow.
1: Clone the template workspace
1.1. Go to the Genomic screening pipeline workspace.
1.2. Click on the three-dot menu at the top-right of the workspace and select Clone.
1.3. Fill in a Workspace name. In this example, I’ve added my initials and the date so it’s easy to identify. Select your Terra Billing project and click the CLONE WORKSPACE button.
What to expect
1.4. Your cloned workspace will take a few minutes to create. You will need to navigate to your cloned workspace (Main menu > Genomic Screening > Polygenic Risk Score) to continue.
2. Examine the workspace data table
2.1. In your cloned workspace, click on the DATA tab.
2.2. The workspace comes with a data table called cohorts. Click on the name to examine the table.
2.3. This table contains one row and six columns of data.
What’s in the cohorts table?
The table includes links to the input files in a Terra workspace’s Azure storage container that will be used as inputs for the Genomic Screening workflow.
3. Run the GWAS-regine workflow
Workflows are orchestrated in Terra by the workflows application - Cromwell. When you are in a new workspace, you will need to launch Cromwell. Note that you only need to do this once, the first time you set up or run a workflow in the workspace.
3.1. Go to the Workflows tab.
3.2. Click the blue Launch Workflows App button.
The Workflows app may take between 5-15 minutes to launch.
When workflows are ready
After a few minutes, you will see the workflows menu on the left-hand side and the GWAS-regine workflow from the original workspace in the center under Workflows in this workspace.
3.3. Click the blue Configure button for the GWAS-Regenie workflow.
3.4. The data table should already be set to the cohorts table. If it is not already selected, choose it from the dropdown menu. Check the box to select the only row in the table.
3.5. The Inputs and Outputs have already been configured for you. You can click on these tabs to see what is configured for each workflow attribute, and what columns will be generated for the outputs.
Inputs configuration screenshot
The workflow will generate a new file, workflow_output. The output file will be written back to the original data table you examined earlier.
Outputs configuration screenshot
3.6. When you’re ready to run the workflow, click the blue SUBMIT button. You can add a comment for this submission if you wish, then click SUBMIT again.
3.7. The first time you run a workflow in your workspace, Cromwell will take some time to launch. The workflow will submit automatically once Cromwell is up and running and you’ll be redirected to the Submission details page.
3.8. You can monitor your submission progress at any time by clicking the Submission history option on the left side of the Workflows page. Clicking the submission name will give you more information.
3.9. Once the submission is complete, you will see the status change to Success. You can click on the Submission name for more details.
4. Find/explore results
4.1. Click on the DATA tab again to examine the cohorts table once more.
4.2. Click to open the cohorts table and scroll to the right to see the newly generated output files that has been added to the table in four new columns.
4.3. Clicking on the link in the pipeline_metadata column will expose where the file is stored in your workspace cloud storage and allow you to download the output file to local storage.