DNAnexus

ElemBio Cloud integrates with DNAnexus as a cloud service provider. The DNAnexus provider supports storage connections, compute activities, and verified flows, such as the Bases2Fastq flow. DNAnexus offers a suite of analysis options, including the Bases2Fastq app and options for secondary analysis. For an example workflow configuration, see the Integrating DNAnexus for FASTQ Automation tutorial.

Requirements

Configuration of a DNAnexus provider requires the following components:

• A DNAnexus project: The project stores run files output from the AVITI System.
• An API token with access to the project: The API token serves as a credential for ElemBio Cloud to transfer data.
• A workflow that uses the Bases2Fastq app: The workflow allows you to execute Bases2Fastq and other analyses. Make sure to note the workflow ID, which the DNAnexus user interface displays when you select a workflow.

For more information on these requirements, see the User Interface Quickstart and Authentication pages in the DNAnexus Documentation.

Configuring ElemBio Cloud

After fulfilling the provider requirements, you can complete the following tasks to configure ElemBio Cloud. The available actions depend on your user permissions.

Add a DNAnexus Provider

1. On the Providers page, select DNAnexus.
2. Enter a unique name.
3. Enter the API token for the DNAnexus project.
4. Select Save to create the provider.

Add a DNAnexus Storage Connection

A storage connection enables you to transfer data to the DNAnexus project you own. Before you create a storage connection, you must set up the provider.

1. On the Storage page, select Add Storage.
2. Select the DNAnexus provider for the storage connection.
3. Enter a unique name.
4. Enter the Project ID.
5. If applicable, enter a Run Upload Folder to indicate a folder structure for run data.
6. Select a Use for Run Upload setting.
   • If you enable the setting, the storage connection becomes available on instruments associated with your organization.
   • If you disable the setting, the storage connection is unavailable on instruments. You can only use the storage connection for ElemBio Cloud activities, such as verified flows.
7. Select Save.

Add a DNAnexus Compute Connection

1. On the Compute Connections page, select Add Compute.
2. Select the DNAnexus provider for the compute connection.
3. Enter a unique name.
4. Select Save to add the compute connection.

Add a DNAnexus Bases2Fastq Flow

1. On the Flows page, select Bases2Fastq Flow.
2. Select the DNAnexus provider for the flow.
3. Enter a unique name.
4. Enter the workflow ID for the intended workflow in your project.
5. In the Bases2Fastq Version drop-down menu, select Always use latest or a specific software version.
6. In the Parameters field, enter the Bases2Fastq optional arguments you want to use.

   The flow applies these arguments to all executions.

7. Select a Trigger option: Automatically on completed runs or Manually trigger on runs.
8. Select a DNAnexus storage connection for Input Storage.
9. Select a DNAnexus storage connection for Output Storage.

   DNAnexus writes data to the project for this storage connection when analysis is complete.

10. Review the Bases2Fastq Terms of Service, and then select the checkbox to agree.
11. Select Save.