Workflow-Run Templates
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Workflow-Run Templates

What is a Workflow-Run Template?

At Form Bio we use the term Workflow to describe a defined set of computational tasks that can be executed with specific input parameters. When someone has provided values for the Workflow’s input parameters (eg. choosing specific files to use, or updating configuration options) and launched the Workflow, we call this a Workflow-Run.

Workflow-Run Templates (or just “Templates” for short) are a defined set of input parameters to make creating Workflow-Runs easier by enabling collaboration and repeatability. Once you have created a Template with specific input values in the Workflow Launcher, you will be able to come back to the Workflow Launcher via that Template to find the same input values set.

Unlike Workflow-Runs, Workflow-Run Templates don’t require that all inputs have a value provided in order to be saved. This allows you to make updates over time instead of all at once.

When is a Template Helpful?

Templates can be helpful in a number of different scenarios, such as:

  • When you want to run the same Workflow configuration, but swap out a file.
  • When two team members are collaborating, one of which is more familiar with the advanced computation side of Workflow configuration, and one on the biological side.
  • When awaiting data to be ready for you, now you’ll be to set everything up for your Workflow Run and then come back to add your data once it’s ready.

How to Create a New Template

First things first, you will need to select the Workflow and Workflow Version you would like to create a Template for.

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Click the Nav item Workflows → Launch to reach the Page above.

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Note: Workflows vs. Workflow Versions

Each Template is scoped to a specific Workflow and Workflow Version. Meaning if I create a new Template for (example) Genomics Variant Analysis v1.7.1, that Template will not be available for Genomics Variant Analysis v1.8.0.

If you or others in your Project have already created Workflow-Run Templates you will now see them appear atop the layout containing Workflows as well. Workflows are distinguished with an orange badge in the top-left corner of the card, whereas Templates have a blue badge.

Once you have selected the Workflow and Workflow Version, you will see a Page resembling the once below. You can make any changes you like to the input values now, though no changes are required for saving a Template.

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Note: What’s that red dot?

If you have made changes to the input values since selecting a Workflow or Template, you will notice a red dot in the corner of the “Save Template” button. This is a friendly reminder you may want to save your progress, as Auto-Save is not enabled.

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Once you’re ready, select the green “Save Template” menu button. If you haven’t saved yet, you’ll see only one option appear - “Save As New…”. Select this option, provide a name for your Template, and press “Save”.

Here are a couple things to keep in mind:

  • Your Template (and its name) are visible to all your Project team members. So you’ll want to choose a name that’s unique and not offensive.
  • You can confirm you are now working on your Template a couple ways:
    • The name you provided your Template will appear in parentheses next to the Workflow Name.
    • When you click the green “Save Template” button you will now a simple “Save” option along with “Save As New…”

🎉 Congrats, you have created your first Workflow-Run Template! You are saving yourself and your team valuable time by creating this reusable Template. Keep reading the other sections in this document to learn what you can do now with your Workflow-Run Template.

How to View Your Team’s Templates

There are two main places to view your Templates:

  1. By Selecting Workflows → Launch you are brought to a familiar page. This page shows Workflows that you can use to create new Workflow-Runs or Workflow-Run Templates, and now also shows the Workflow-Run Templates your team has already created.
    1. You can use the “All / Workflows / Templates” tabs in the top left to toggle between seeing just Workflows/Templates individually, or both together. You can also search through the Templates by typing in a name of the Template you’re looking for, or filter the view by selecting a Workflow Category. You’ll notice that Templates adopt the Categories of the Workflow they map to.
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  2. You can select “Templates” from the left-side Nav Menu to see a consolidated table view of all the Templates for your Project. We’ll highlight the actions you can take from this view in the following section, but it’s worth noting that clicking on the row anywhere except the menu or star button at the end will bring you to the “Workflow Launcher” view for that Template.
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How to Update or Delete a Template

Update Name or Delete Template

First you will need to navigate to the Template Management Page, which can be accessed only by clicking “Templates” on the left-side Nav Menu.

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Once here, click the three-dot menu in the right-most column in the row of the Template you wish to update. Select whether you would like to “Change Name” or “Delete Template”.

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 Note: Is Delete Permanent?

Yes, deleting a Template is a permanent, irreversible action, so be sure you would like to delete the Template. Don’t worry though, that “Delete Template” menu button has a safety mechanism. You will be prompted to confirm or cancel your decision before the deletion occurs.

In the case of a rename action, simply provide a new name in the pop up window and press “Update” to submit your change. You should see the new name reflected immediately, and your updated Template will be shifted to the top of the table if you haven’t changed how the table is sorted.

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Update Template Input Values

Choose the Template you wish to update from either the Workflow Selection or Template Management Page. Once selected, you will be navigated to the Workflow Launcher “Review” Page. If the Template you selected is missing required fields like the one in the image below, you will see that highlighted in red too.

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Select “Make Changes” aside the group you would like to update to navigate to that group, or select it from the tabs at the top of the page. Make updates to one or many groups, and then press “Save Template” and “Save” to overwrite the old state of the Template.

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Note: What if I don’t want to save the changes I just made?

If you decide against the changes you’ve made, you can select “Close” from the top right, and proceed without saving. As long as you haven’t pressed “Save Template” and “Save” yet, the Template will be in its original state when you revisit it.

If you have already made changes and saved them, you will have to undo those changes and save again. Now if you want to avoid running into that particular scenario, read the next section.

How to Copy a Template

Choose the Template you wish to update from either the Workflow Selection or Template Management Page. Once selected, you will be navigated to the Workflow Launcher “Review” Page.

Select the green “Save Template” button, then choose “Save As New…”, provide a name for the new Template, and submit. You’ll see that all the values from your original Template are still shown for its copy. Any changes you make and save will be saved to the new Template and not affect the original.

How to Run a Workflow from a Template

It is important to note that Workflow-Run Templates do not require all input parameters to have a value set. However, Workflows may require that all or some particular input parameters have values before running the Workflow (ie. Creating the Workflow Run).

Just as with running a Workflow prior to the Templates feature, you can visit the “Review & Submit” tab of the Workflow Launcher in order to see what required fields are missing a value, and navigate to a form that allows you to set those values.

As long as all required inputs have values set, you can run a Workflow by selecting “Run Workflow” on the Review & Submit page of the Workflow Launcher.

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Note: Does my Template go away when I create a Workflow Run?

No, your Template will not disappear when a new Workflow Run is created. However, it is important to note that your Template won’t be saved when you select “Run Workflow” either. So if you see a red dot on the “Save Template” menu button and want all the input values to be saved to your Template, be sure to take that action before selecting “Run Workflow”.

Uh-oh, too late?

Don’t worry! Another new Form Bio feature has you covered. Read how you can use a Workflow Run to populate the Workflow Launcher here, and apply what you’ve learned about creating and managing Templates to store those changes for later if you like.