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Register a Workflow on Dockstore

Tutorial Goals

  • Discover how to register a workflow on Dockstore
  • Publish your workflow

This tutorial walks through the process of registering and sharing more complex workflows which are usually comprised of multiple tools, strung together in some sort of order (often a directed acyclic graph (DAG)). Workflows also differ from tools since they are not required to define their own environment. Instead, a workflow engine like Arvados or Cromwell, or an infrastructure like Galaxy will provide the ability to execute a CWL, WDL, or Galaxy workflow respectively.

This tutorial does not go through the creation of a workflow and its registration to GitHub, Bitbucket or GitLab. It assumes that you already have a repository which contains a workflow and are now trying to register it in Dockstore.

Register Your Workflow in Dockstore

There are a variety of ways to get your workflows into Dockstore. GitHub App registration is the recommended way to register for all new workflows on Dockstore using GitHub. The legacy registration process is used for Bitbucket and GitLab.

Register Your Workflow to Automatically Sync with GitHub (Recommended)

This is the newest way of getting content onto Dockstore and is by far the most automated. Using GitHub Apps, Dockstore can react to changes on GitHub as they are made, keeping Dockstore synced with GitHub automatically.

Once you've installed our GitHub app on a repository in an organization or your personal account, you'll need to add a dockstore.yml file to the root directory of a branch of the repository that contains your workflow. This file contains information like workflow path, test parameter file, workflow name, etc. When a push is made on GitHub to a branch with a .dockstore.yml, Dockstore will add that branch to the corresponding workflow on Dockstore. If the workflow doesn't already exist on Dockstore, one will be created (but will not automatically be published publically). Note that a single dockstore.yml file can describe multiple workflows, if all of those workflows are in the same repository.

Note

For Galaxy workflows it is recommended you use the Galaxy command-line utility, Planemo, to generate the .dockstore.yml. See Generating a .dockstore.yml with Planemo <Planemo dockstore.yml>

Below is a simple example of a .dockstore.yml file for an alignment workflow to show you how easy it is to use. Note that all file paths in the file must be absolute.

version: 1.2
workflows:
   - subclass: CWL
     primaryDescriptorPath: /aligner.cwl
     testParameterFiles:
     - /test/aligner.cwl.json
     topic: A short descrption of this workflow

If you had our GitHub App installed on the repository myorg/alignments and then add the above .dockstore.yml to the develop branch, the following would occur:

  • A CWL workflow with the ID github.com/myorg/alignments will be created on Dockstore
  • The version develop is added to the workflow github.com/myorg/alignments
  • The version has the primary descriptor file set to /aligner.cwl
  • The version has one test parameter file: /test/aligner.cwl.json

Now that your workflow has been added, any time there is a push to a branch on GitHub for this repository that has a .dockstore.yml, it is automatically updated on Dockstore! Anytime there is a deletion of a branch on GitHub that has a .dockstore.yml, the version is removed from Dockstore.

For more information on this method, as well as general troubleshooting advice, please check our Dockstore GitHub Apps Overview </getting-started/github-apps/github-apps> page.

Legacy Registration Methods

If you are using BitBucket or GitLab and would prefer not to use GitHub, or if you are using GitHub but do not wish to install our app, our legacy registration methods have you covered. Several options are available to you and described in our legacy registration methods documentation </advanced-topics/legacy/workflow-legacy-registration>.

Sharing Your Workflow

For Terra Users : You have the ability to share hosted workflows through Dockstore. This allows for you to share workflows wth other users who have used their Google account to register on Terra. Learn more at Workflow Sharing <../advanced-topics/sharing-workflows/>.

Next Steps

You may not want to store your files directly with a service like GitHub. Perhaps you want your descriptor files to not be public. The solution is to use Hosted Tools and Workflows </getting-started/hosted-tools-and-workflows/>.