Importing Workflows

Users can import external workflows to simplify their data analysis process.

Importing External Workflows

You can access the Importing External Workflows form through the Tools tab on the global menu:

Accessing the Import External Workflow Form

On the Importing External Workflows form, enter the URL of the external workflow, and select the project within which you'd like to use it:

Converting Existing Workflows

Bash scripts can be used to run workflows on the DNAnexus Platform. But they are inefficient when scripts need to be run more than once, or shared among collaborators.

To facilitate reproducibility in working with data, the DNAnexus Platform supports the use of WDL and Nextflow workflows.

Converting scripts to WDL workflows ensures reproducibility and allows your workflows to be easily published and shared. Use dxCompiler to compile WDL workflows so that they can be run on the Platform.

Use the Nextflow for DNAnexus app to deploy Nextflow pipelines on the DNAnexus Platform. Note that a Nextflow license is required to use this app.

The workflows mentioned above can also be run on the Cloud Workstation and in a Jupyter notebook. R and Python scripts can be run in these contexts as well, but can also be turned into applets or apps. Turning scripts into applets or apps allows for efficient GUI/CLI deployment, and allows for integration with modular workflows.

Git, Conda and Docker are provisioned in the DNAnexus JupyterLab environment, while Git and Docker are available on Cloud Workstation (Conda can be added, e.g. through Miniconda).

Workflow Tutorials

Below are a couple of links to help get you started on working with creating and importing workflows from different languages and sources to the DNAnexus Platform.

Running Imported Workflows

Running imported workflows is very similar to running workflows that you have created yourself. See documentation here for more details.