Configuring an existing repository of workflows (with alternative versioning method)


We have a public repository at umccr/cwl-ica: A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide ( we’d like to connect / and share with Dockstore. CWL Workflows and tools are organised by workflows/<workflow_name>/<workflow_version>/<workflow_name__<workflow_version>.cwl. So I’m not sure if the versioning would be compatible with the DockStore versioning that is done by git tag.

Any help on how we could implement this would be fantastic!

Kind regards,

Thanks for your question! We’ve been discussing your request and looked over the repo you linked. We do try our best to make use of common git practices to support versioning in Dockstore and did not think of your usage. You can currently add tools manually, but at this time we don’t have a good solution for workflows.

For more information on organizing your repo please have a look at Best Practices for Secure and FAIR Workflows — Dockstore documentation

Thanks for the prompt reponse David, we’ve justified our structure for CWL workflows here: Best_Practises · umccr/cwl-ica Wiki (

What is the process for uploading tools / workflows manually. We have integrated much of our automation processes in ICA with GitHub Actions so could do the same for Dockstore.

Kind regards,

We’d like to help you get your workflows on Dockstore if we can! Please take a look at Manual Registration of Workflows and Manual Registration of Tools.

Although we encourage people to use the .dockstore.yml method for maintaining content from GitHub, there may be a way path forward using CI and Dockstore API endpoints. For example, you may be able to manually create your workflows initially and then use the created identifier to issue subsequent updates to the workflow from your CI jobs. If you end up going down this route you may find the Dockstore CLI and API descriptions useful (updateWorkflowVersions and manualRegister).