Migrating Your Existing Workflows to Use GitHub Apps

Dockstore 1.9.0 provides users with a way to keep their workflows automatically updated (instead of needing to manually refresh) by using GitHub apps. Here, we will go over how to migrate your existing Dockstore workflows to use GitHub apps. This tutorial assumes that you are are familiar with the /.dockstore.yml file by having read our overview of GitHub apps. and the Registration With GitHub Apps section in our workflow registration document.

GitHub App Installation

The first step to migrating a workflow is the same as adding a new workflow via GitHub apps: install our Dockstore GitHub app onto your repository or organization. You do this by navigating to /my-workflows, clicking the + button on the left hand sidebar, selecting Register using GitHub Apps, and then clicking + Manage Dockstore Installation on GitHub. You’ll then be redirected to GitHub where you can select which repositories can be accessed by the GitHub app.

../../_images/add-workflow-button.png ../../_images/register-workflow-github-apps.png ../../_images/gh-app-reg-1.png

Creating a .dockstore.yml File

Once the GitHub app is installed on the correct repo, the next step is to create a /.dockstore.yml file. We’ll cover a very straigtforward example first, but depending on how you configured the workflow during registration and whether your GitHub repository houses multiple workflows published on Dockstore, there will be additional steps to writing your /.dockstore.yml file.

Let’s say we have the following CWL workflow registered on Dockstore that came from this repository and you would like to convert the master branch.

Workflow to Migrate

As noted in our other documentation, create a /.dockstore.yml file in the root directory of the branch you want to migrate (in this example, it’s the master branch) in your repository. The file should look like the following

version: 1.2
workflows:
   - subclass: CWL
     primaryDescriptorPath: /Dockstore.cwl
     testParameterFiles:
         - /test/dockstore.cwl.json

The information above was filled out using the following:

  • subclass is taken from the Descriptor Type
  • primaryDescriptorPath is from Workflow Path
  • testParameterFiles is from Test File Path

During the original registration for your workflow, you may have filled out the Workflow Name field shown in the picture below.

Workflow to Migrate

This field is required when you want to register multiple workflows from the same repo, but you may have filled it out for other reasons. To check if the workflow you want to migrate has a workflow name set, select the workflow and look at the title on top as shown in the picture below.

The title consists of: <sourceControl>/<organization name>/<repository name>/<optional workflow name>:<version name>

If you see a workflow name inserted, you must include the name field in your /.dockstore.yml.

version: 1.2
workflows:
   - subclass: CWL
     primaryDescriptorPath: /Dockstore.cwl
     testParameterFiles:
         - /test/dockstore.cwl.json
     name: optional-name

If you have multiple workflows registered on Dockstore that stem from the same GitHub repo, a single /.dockstore.yml can be used to convert them. Again, you need to check for the Workflow Name field being set because it’s need for multi workflow repositories. If the name field in the dockstore.yml doesn’t match the Workflow Name field in Dockstore, the migration of your workflow on Dockstore will not go through and it will instead create a new Dockstore entry. Let’s say we want to convert these two workflows that come from this repository.

../../_images/github-apps-multiple-workflows.png ../../_images/github-apps-multiple-workflows-with-name.png

Your /.dockstore.yml would look like the following:

version: 1.2
workflows:
   - subclass: CWL
     primaryDescriptorPath: /Dockstore.cwl
     testParameterFiles:
         - /test/dockstore.cwl.json
   - subclass: WDL
     primaryDescriptorPath: /Dockstore.wdl
     testParameterFiles:
         - /test/dockstore.wdl.json
     name: optional-name

Testing the Migration

Note

Push events will only be captured by Dockstore after installing the GitHub app onto the repo.

To test out your GitHub app integration, make a push to a branch. Navigate to or refresh your browser on the My Workflows page, and select the workflow you wanted to convert. You should see that the Workflow Information section looks a bit different.

../../_images/workflow-information-after-migration.png

It now lists the mode as DOCKSTORE_YML instead of FULL and information about paths is no longer included. You are also no longer able to refresh or restub the workflow any more. Since you can’t refresh the entire workflow anymore, new versions from GitHub (releases/branches) that you want to add to Dockstore must have a DOCKSTORE_YML. However, you can still refresh already existing versions/branches on Dockstore that you haven’t converted by going to the Versions tab, clicking Actions, and selecting Refresh Version.

See also

Troubleshooting and FAQ - tips on resolving Dockstore GitHub App issues.