How to set up and run a workflow

Allie Cliffe

This article walks through the setup process for running a workflow in Terra on Azure when using inputs (data samples) from a data table. Please note that this document only includes functionality available for public preview.

Overview: Workflows in public preview (current functionality)

For the public preview, you can try out running a workflow by creating a workspace. All Terra on Azure workspaces include three pre-staged workflows.

For step-by-step instructions to run the three workflows as a complete analysis, see the Covid-19 Surveillance Featured Workspace and accompanying Guide

Step 1: Copy workspace and launch data tables infrastructure

1.1. Go to Your Workspaces (select from the main navigation menu at the top left of any page).

1.2. Create a workspace by clicking on the Create Workspace button at the top of the page.

What to expect

Once you create a new workspace, Terra will automatically launch the cloud infrastructure to power data tables. 

When data tables are ready

Once data tables are launched, you’ll see the active import data button in the top left section of the Data page.

Step 2: Set up Cromwell (the workflows application)

You will need to take a few additional steps to launch the workflows application (Cromwell)

2.1. Click on the cloud icon in the right sidebar. 


2.2. Click the gear icon under the Cromwell logo in the Cloud Environment Details pop-up. 


2.3. Click the blue Create button in the Cromwell Cloud Environment pop-up. 


When workflows are ready

After a few minutes, you will see the little pig icon for Cromwell in the right-hand sidebar with a little green dot that shows it’s ready to use.


It may take several minutes to requisition and set up the cloud infrastructureBoth data tables, and Cromwell must be ready before you can move on to the next step. See Data tables: Additional resources for more details about the Workspace Data Services that power data tables.

Step 3: Upload data table (optional)

Terra workflows are set up to pull inputs (URIs for data files in open-access Azure blob storage containers) from the data table. If you cloned a workspace that already had a table in it and used a billing project created after August 2nd, 2023, you should see the table as soon as your Workspace Data Services infrastructure loads.

If you don't have a table, will first need to generate the input data table by uploading a pre-staged TSV. You can create a TSV from scratch in a spreadsheet, or download one from an existing Terra on Azure workspace, following the directions below. 

3.1. Click on the three-dot action icon beside the table you want to add to your own workspace and select Download TSV


3.3. Click the save button to download the TSV to local storage. 


3.4. Navigate back to the Data page of your own workspace

3.5. Click the Import Data button (left side near the top) and select the Upload TSV option to create and populate the data table.


3.6. In the Import Table Data popup, fill in the table name and select the TSV you just downloaded.  


3.7. Click the Start Import Job button. 

What to expect

You should see your data is now visible in the tables section of the Data page


Step 4: Launch the Cromwell app

When the workflows infrastructure is ready, the button on the Cromwell logo on the right sidebar will turn green, and you can launch the Cromwell app (in a separate tab).

4.1. Click the Cromwell icon (right sidebar).


4.2. Click Open to open a new Workflows window in a separate tab.

You’ll see cards for three pre-staged workflows.


What do the three pre-staged workflows do?

  1. Pull in SARS-CoV2 data from NCBI’s Sequence Read Archive (SRA)
  2. Perform reference-based assembly
  3. Create visualizations using NextStrain

Step 5: Add a workflow

In addition to the three pre-configured workflows, you can select from a number of workflows in Terra directly, or import workflows from GitHub. 

5.1. In the Cromwell tab, click on the Find a Workflow button to surface the modal below.


Option 1: Browse suggested workflows

5.2. Click on one of five suggested workflows to reveal the configuration card.

Once you click on a suggested workflow, you will see it in the Workflows tab

Option 2: Add a workflow (GitHub)

5.2. Select the Add a Workflow link.

5.3.Fill in the GitHub link and workflow name in the blank fields and click the Add to Workspace button (the button will be disabled if every field is not filled in).


5.4. You will be directed to the submission configuration form, where you can set up and run your workflow.

What to expect

Any time you go to the Run workflows with Cromwell tab (by clicking on the Cromwell icon in the right sidebar and clicking Open), you will see the new workflow in the list. 

Step 6: Select data and set up the workflow

Click on the workflow card (for example, fetch_sra_to_bam - one of the three pre-staged workflows) to access the submission configuration form


What to expect

The configuration form includes useful information like the workflow version and source URL link. It is also where you will set up the workflow to run on specific data from the input table. 

5.1. Select the input data table

Choose the table with the input data files from the dropdown.

5.2. Select data rows to run on

1. Navigate to Select Data at the bottom of the form to see the data table.

2. Select the rows to analyze by clicking the checkbox at the left of the row.


5.3. Specify input variable attributes

Go to the Inputs tab to specify data table columns (attributes) for each variable. Choose Fetch from Data Table as the Input source and select each variable's attribute from the dropdown.  ToA_Configure-inputs-in-configuration-pane_Screenshot.png

Note on configuring inputs

Note you can select input sources (hard coded or from the data table) for each variable. If you choose to Fetch from table, the attribute column dropdown will display all columns in the data table.  

5.4. Write outputs to the data table

Next, click Outputs to configure the workflow to write a new column to the sample data table for each output variable. You can enter a new name in the attribute column to make a new column. 


Where is generated data stored?

Generated files will be stored in the workspace blob storage container by default. When the output attribute is filled in, Terra will write the file locations (URIs) of generated files in a new column in the input data table.

Step 6: Submit the workflow

6.1. When ready, select Submit to open a popup window where you can name and enter comments about the submission.


Your submission has a pre-populated name that includes the workflow name, input data table, and date and time of submission. You can change this to be meaningful to you.

The popup includes how many workflows will be submitted in this submission.

6.2. To confirm and launch the workflow submission, click the Submit button again.

What to expect

Once you submit, Terra will get to work setting up and deploying the cloud resources to run your workflow. You will automatically be directed to the submission details page.

Next steps: Monitor workflow submission status

The submission details page of the Cromwell environment includes the workflow name, submission date, and duration.

How to find the Submission HistoryNote that the Submission History and submission details pages are in the Cromwell environment, which is distinct from your workspace pages. If you cannot see the submission history option, make sure you have Cromwell running (green icon in the right sidebar from any workspace page) and are in the Cromwell environment (separate tab from the workspace). 

At the bottom of the page is a list of all the workflows in the submission (running in parallel), along with the sample ID, workflow ID, status, and duration.


To see the status of a workflow, its start and end time, and sub-workflow and task failures, click on an individual workflow ID to view the workflow details page.

Use the breadcrumb on top of the page (circled in the screenshot below) to navigate back and forth between the submission history (lists of previous submissions), submission details page, and workflow details page.


What to expect (completed workflows)

When the workflows are done, and you see a green check in the Job History, you can verify that the generated output files are in your workspace blob storage container by clicking on the Files icon in the right sidebar. This will open the directory of your workspace storage. 

To access the generated data files

Click in the left-hand column to open the subdirectories cromwell-executions > workflow-name > submission-ID > taskname > execution > output file. You will see a list of all the generated files. 


Note that you may need to go down several levels in the file directory to find the data files. 

How to abort a workflow

There are many reasons you may want to abort a running workflow. Perhaps you included a wrong input or have a failed task that you debugged and now want to abort, make the edits, and re-submit. 

In the Submission History page, click on the three-dot action icon to see the abort workflow option.


Was this article helpful?



  • Comment author
    Curtis Kapsak

    FYI I ran into a broken link in this guide.

    For Step 2.1, when I try to click the link to download the sample TSV file, I'm met with an authentication error and no TSV file is downloaded.


    When I navigate to the featured workspace to try to download the TSV, it looks like the data table service is not up and running:

    Perhaps this is why I'm unable to download the sample TSV file?

  • Comment author
    Allie Cliffe

    I'm so sorry you couldn't download the TSV Curtis Kapsak! The data table status in the Featured Workspace doesn't affect whether you can access the file. The table status error you saw was because tables were single-user and only viewable to workspace creators until last week. 

    But I'm glad you commented since you revealed a problem with our instructions (and I have updated them, so they should be current). You should be able to see the sample table in the Featured Workspace now. If you click on the three-dot action icon to the right of the sample table, you can download the sample.tsv to your local machine, then upload it to your own workspace copy. 


Please sign in to leave a comment.