End-to-End User Flow: DRAGEN Analysis

This tutorial demonstrates major functions of the ICA platform, beginning with setting up a project with instrument run data to prepare to use pipelines, and concluding with viewing pipeline outputs in preparation for eventually ingesting outputs into available modules.

In the following example, we start from an existing ICA project with demultiplexed instrument run data (fastq), use the DRAGEN Germline pipeline, and view output data.

Set-up

This tutorial assumes you already have an existing project in ICA. To create a new project, please see instructions in the Projects page.

Additionally, you will need the DRAGEN Demo Bundle linked to your existing ICA project. The DRAGEN Demo Bundle is an an provided by Illumina with all standard ICA subscriptions and includes DRAGEN pipelines, references, and demo data.

Linking an Entitled Bundle

For general steps on creating and linking bundles to your project, see the page. This tutorial explores the DRAGEN Germline Published Pipeline, so we will need to link the DRAGEN Demo Bundle to our existing project.

Steps:

• Go to the Projects > your_project > Project settings > Details page

• Click Edit

• Click the + button, under Linked bundles

DRAGEN Demo Bundle assets will now be available on the Data and Pipelines pages.

Pipelines

After setting up the project in ICA and linking a bundle, we can run various pipelines.

DRAGEN Germline Published Pipeline

This example demonstrates how to run the DRAGEN Germline Published Pipeline (version 3.9.5) in your ICA project using the demo data from the linked DRAGEN Demo Bundle.

The required pipeline input assets for this tutorial include:

• Under Projects > your_project > Data

  • Illumina DRAGEN Germline Demo Data folder

  • Illumina DRAGEN Enrichment Demo Data folder

Launching the DRAGEN Germline Published Pipeline with Demo Data

From the Projects > your_project > Flow > Pipelines page, select DRAGEN Germline 3.9.5, and then click Start analysis. Initial set-up details require a User Reference (pipeline run name meaningful to the user) and a Subscription from the drop-down menu under Pricing.

Running the DRAGEN Germline pipeline uses the following inputs which are to be added in the Input Files section:

The DRAGEN Germline Settings should match:

Once all parameters have been set, click Start analysis

Monitoring analysis run status

You can monitor the status of analysis pipeline runs from the Projects > your_project > Flow > Analysis page. See for more details.

Click the refresh button () in upper right corner of the ICA environment page to update the status.

Click on the run to view more information about it. The various tabs under a given run provide additional context regarding the status of the completed run.

If you encounter a failed run, you can find more information in the Projects > your_project > Flow > Analyses > your_analysis > Details tab and on the Nextflow execution tab.

Analysis run logs can be found on the Steps tab. Use the sliders next to Stderr and Stdout for more details. Check the box next to Show technical steps to view additional log files.

Viewing DRAGEN analysis output

DRAGEN analysis output folders are found on the Projects > your_project > Data page, along with all other data loaded to the project (such as assets from a linked entitled bundle). Output analysis will be grouped into folders, so you can click through the folder structure to explore outputs.

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