Importing Workflows

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

To import a workflow onto the DNAnexus Platform, choose a project for the imported workflow to reside in. Once you are in Manage tab of your project, click the Add button and from the dropdown select Import Pipeline/Workflow.

On the Import Pipeline/Workflow form, enter the URL of the external workflow, and select the folder where the workflow will be imported:

Converting Existing Workflows

Bash scripts can be used to run workflows on the DNAnexus Platform, but they can be 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 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.

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 resources to help get you started on working with creating and importing workflows from different languages and sources to the DNAnexus Platform.

• Converting WDL Workflows: dxCompiler

• Using WDL to Develop Locally and Scale to the Cloud (Webinar)

• Turning R/Python scripts into applets: Applet building

Running Imported Workflows

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

Importing Nextflow Workflows

For detailed information on how to import and run a Nextflow workflow, see Running Nextflow Workflows.