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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.

Configuration​

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​

For information on adding a Bases2Fastq flow, see the information on the page for the provider:

Reexecute a Bases2Fastq Flow​

Reexecuting a Bases2Fastq flow allows you to resolve errors, address quality issues, apply new optional arguments, or use a corrected run manifest. You can reexecute from the Actions column on the Executions page or in the FASTQ tab of a Run Details page.

  1. Select Reexecute or Reexecute Flow.
  2. When prompted, select the run manifest for the reexecution.
    1. Select Browse, and then browse to the run manifest file.
    2. Select the run manifest file, and then select OK.
  3. Enter any optional arguments in the Parameters field.

    For example, to add the QC only mode optional argument, enter --qc-only.

  4. Select Execute Flow.
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