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Bases2Fastq Flow

Bases2Fastq flows use the Bases2Fastq software in a single-step pipeline to generate cloud-hosted FASTQ files.

ElemBio Catalyst includes a Bases2Fastq flow that Element sets up for you, which you can then edit to customize. The following providers also allow you to configure a Bases2Fastq flow:


A Bases2Fastq flow has the following configuration settings:

  • Bases2Fastq Version: Sets the Bases2Fastq software version for the flow.
    • Latest automatically upgrades the flow to the most recent version of Bases2Fastq. Selecting this option can cause executions to use different Bases2Fastq versions.
    • Selecting a specific Bases2Fastq version allows the flow to always execute with the same version and maintain stability between executions.
  • Parameters: Applies any Bases2Fastq optional arguments globally to all executions of the flow. For example, to use QC-only mode for all executions, enter --qc-only.
  • Trigger: Options let the flow automatically execute when a run completes or require you to manually start executions from the FASTQ Files tab on Run Details pages.

Add a Bases2Fastq Flow

  1. On the Flows page, select Bases2Fastq Flow.
  2. Select the provider for the flow.

    If you are using Amazon HealthOmics, make sure the provider is associated with a JSON policy with the necessary permissions for Amazon HealthOmics.

  3. Enter a unique name for the flow.
  4. Enter the details for your provider type.
    • For Amazon HealthOmics, enter the ARN of the IAM role that serves as the execution role for the analysis.

      Make sure the role is associated with an JSON policy for an execution role.

    • For DNAnexus, enter the workflow ID for the intended workflow in your project.
    • For Seqera, enter the ID for the compute environment.
  5. In the Bases2Fastq Version drop-down menu, select Latest or a specific software version.
  6. In the Parameters field, enter the Bases2Fastq optional arguments you want to use.
  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.
  10. Review the Bases2Fastq Terms of Service, and then select the checkbox to agree.
  11. Select Save.