Getting started with HealthOmics

To get started with HealthOmics, ensure that you have properly set up your IAM permissions and roles for HealthOmics.

Using a Ready2Run workflow in the HealthOmics console

The following exercise shows how to use a Ready2Run workflow. A Ready2Run workflow is preconfigured with the parameters and tool references you need to run the workflow. The workflow publisher provides sample data, so you do not need to create your own data.

1. Open the HealthOmics console.

2. Select the navigation pane (≡) in the top left, and select Ready2Run workflows.

3. On the Ready2Run workflows page, choose the ESMFold for up to 800 residues workflow. The console opens the details page for that workflow.

4. The details tab provides information about the workflow. To try out the workflow, in the top right of the page select Start run.

5. In the Specify run details page, enter a run name.

6. Enter or select an Amazon S3 location for the run output.

7. For Run metadata retention mode, choose whether to retain or remove runmeta data.

8. In the Service role panel, choose Create and use a new service role.

9. Choose Next.

10. On the Add parameter values page, choose Run workflow with Ready2Run test data.

11. Choose Next.

12. Review your inputs, then choose Start run.

Example prompts for Amazon Q CLI

Amazon Q CLI can run genomic workflows and analysis tasks in AWS HealthOmics using natural language commands. The following example prompts allow you to create workflows, manage runs, and analyze genomic data. For more information and example prompts for HealthOmics, see the HealthOmics Agentic generative AI tutorial on GitHub.

• "Create a WDL 1.1 workflow file as main.wdl that will run on HealthOmics. The workflow will take a reference genome as an input and pairs of fastq files. It will index the reference genome using BWA and then map each pair of fastq files to the reference. Finally merge each mapped BAM to a single BAM file and output this file and it's bai index."

• "Package the workflow and create it in HealthOmics"

• "Update the inputs.json file to use real files from my Amazon S3 bucket omics-my-bucket-with-genome-data" (Provide a specific Amazon S3 bucket location, or let Amazon Q explore)

• "Find suitable containers in my Amazon ECR repositories and update inputs.json to use these"

• "Find or create a suitable IAM role to use when running the workflow"

• "Create a run cache for my workflow"

• "Run the workflow in HealthOmics"

• "Check the status of the run"

Warning

When working with Amazon Q CLI, review all generated content and proposed actions before proceeding. Provide feedback to improve response quality and to match your workflow’s requirements. For more information, see Security considerations and best practices for Amazon Q.