AWS HealthOmics MCP Server: Setup for Claude, Cursor and Other Apps

• Lists your HealthOmics workflows

  Lists the HealthOmics workflows in your account, with paging.

  Try: “List my HealthOmics workflows.”

  Read · ListAHOWorkflows

• Shows one workflow and its definition

  Returns details of a workflow and can export its definition.

  Try: “Show the definition of my variant-calling workflow.”

  Read · GetAHOWorkflow

• Creates a workflow from WDL, CWL or Nextflow

  Creates a workflow from a ZIP file, an S3 location or inline content.

  Try: “Create a Nextflow workflow from the ZIP in s3://my-bucket/rnaseq.zip.”

  Write · CreateAHOWorkflow

• Checks a WDL or CWL file for errors

  Runs lint checks on a single WDL or CWL workflow file using miniwdl and cwltool.

  Try: “Lint this WDL file before I upload it.”

  Runs code · LintAHOWorkflowDefinition

• Starts a workflow run

  Starts a run with the parameters, resources and tags you set. Runs use compute that is billed to your account.

  Try: “Start the variant-calling workflow on sample NA12878.”

  Write · StartAHORun

• Lists workflow runs

  Lists runs, filtered by status and date.

  Try: “Show failed runs from the last three days.”

  Read · ListAHORuns

• Shows details of one run

  Returns the status and metadata of a run.

  Try: “What is the status of run 1234567?”

  Read · GetAHORun

• Explains why a run failed

  Looks over a failed run and suggests fixes.

  Try: “Why did run 1234567 fail?”

  Read · DiagnoseAHORunFailure

• Shows logs for a run

  Returns high-level logs and events from a workflow run.

  Try: “Show the logs for run 1234567.”

  Read · GetAHORunLogs

• Analyzes run speed and resource use

  Studies run data to find slow tasks and tasks that used too little or too much CPU and memory.

  Try: “Which tasks in run 1234567 were the bottleneck?”

  Read · AnalyzeAHORunPerformance

• Finds genomics files across stores

  Searches S3 buckets, HealthOmics sequence stores and reference stores for files such as FASTQ, BAM and VCF.

  Try: “Find the FASTQ files for NA12878.”

  Read · SearchGenomicsFiles

• Bundles workflow files into a ZIP

  Packages workflow files into a base64-encoded ZIP for upload. It can also write the ZIP to a local file or an S3 location you give it.

  Try: “Package the files in ./pipeline for HealthOmics.”

  Write · PackageAHOWorkflow

• Imports genomic files into a sequence store

  Starts a job that copies genomic files from S3 into a sequence store.

  Try: “Import the FASTQ files in this S3 folder into my sequence store.”

  Write · StartAHOReadSetImportJob

• Starts many runs of one workflow

  Starts a batch of runs of one workflow with an IAM role and an S3 output location. The runs use compute billed to your account.

  Try: “Start a batch run of workflow 1234567 for these ten samples.”

  Write · StartAHORunBatch

• Cancels a batch of runs

  Cancels a batch of workflow runs.

  Try: “Cancel batch abc123.”

  Write · CancelAHORunBatch

• Deletes all runs in a batch

  Deletes every run that belongs to a batch. This is the one that removes the runs, not just the batch record.

  Try: “Delete all the runs in batch 7654321.”

  Delete · DeleteAHORunBatch

• Deletes a run batch

  Deletes the metadata of a run batch. The runs in the batch are not deleted.

  Try: “Delete batch abc123.”

  Delete · DeleteAHOBatch

• Deletes a HealthOmics configuration

  Deletes a configuration used for workflow runs.

  Try: “Delete the old test configuration.”

  Delete · DeleteAHOConfiguration

Watch out for

• It can start runs that cost money

  Starting runs and run batches uses HealthOmics compute billed to your account. Ask it to confirm the workflow and sample before it starts.

• It can delete runs, batches and configurations

  DeleteAHORunBatch deletes every run in a batch. DeleteAHOBatch and DeleteAHOConfiguration remove records. Use an AWS profile without delete permissions if you do not need them.

• It can change container registry access

  Container tools can clone images into ECR and grant HealthOmics access to repositories. Review these changes in your account.

• The workflow linter runs on your computer

  The lint tools run miniwdl and cwltool locally on the files you point at.

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