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Seqera

ElemBio Cloud integrates with Seqera as an analysis development platform. The Seqera provider in ElemBio Cloud supports compute activities that can execute compatible verified flows from ElemBio Cloud, such as the Bases2Fastq Flow. Because Seqera can only serve as a provider for flows, you must configure a separate AWS or GCS provider for a storage connection.

Requirements​

Configuration of a Seqera provider with a verified flow requires the following components:

  • An organization on Seqera
  • A workspace for the organization
  • A compute environment within the workspace
  • An access token for a user associated with your organization

For more information on the requirements, see the Workspace Management and Seqera Platform API pages of the Seqera Docs.

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 Seqera Provider​

  1. Review the requirements for a Seqera provider.
  2. On the Providers page, select Seqera.
  3. Enter a unique name.
  4. Enter the Workspace ID of the workspace for executions.
  5. Enter your Organization ID.
  6. Enter the access token generated in Seqera for the user associated with your organization.
  7. Select Save.

Add a Seqera Compute Connection​

  1. On the Compute Connections page, select Add Compute.
  2. Select the Seqera provider for the compute connection.
  3. Enter a unique name.
  4. Select the compute environment ID where the workflow executes.
  5. Select Save.

Add a Seqera Bases2Fastq Flow​

  1. On the Flows page, select Bases2Fastq Flow.
  2. Select the Seqera provider for the flow.
  3. Enter a unique name for the flow.
  4. Enter the ID for the compute environment.
  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 storage connection for Input Storage.
  9. Select a storage connection for Output Storage.

    Seqera writes data to the bucket for this storage connection when analysis completes.

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