73 tools from the AWS HealthOmics MCP Server MCP Server, categorised by risk level.
View the AWS HealthOmics MCP Server policy →AnalyzeAHORunPerformance Analyze AWS HealthOmics workflow run performance and provide optimization recommendations.
This tool analyzes HealthOmics workflow runs to help us... CheckContainerAvailability Check if a container image is available in ECR and accessible by HealthOmics.
Queries ECR to determine if a specific container image exists in a r... CloneContainerToECR Clone a container image to a private ECR repository for HealthOmics use.
This tool copies a container image from an upstream registry (Docker Hub,... GetAHOBatch Get details of a specific HealthOmics batch.
Args:
ctx: MCP context for error reporting
batch_id: ID of the batch to retrieve
aws_prof... GetAHOConfiguration Get details of a specific HealthOmics configuration.
Args:
ctx: MCP context for error reporting
name: Configuration name
aws_profile: ... GetAHOReadSetExportJob Get details about a read set export job.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID of the sequence store
ex... GetAHOReadSetImportJob Get details about a read set import job.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID of the sequence store
im... GetAHOReadSetMetadata Get metadata for a specific read set in a HealthOmics sequence store.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID... GetAHOReferenceImportJob Get details about a reference import job.
AWS HealthOmics allows only one reference store per account per region.
If reference_store_id is not pro... GetAHOReferenceMetadata Get metadata for a specific reference in a HealthOmics reference store.
AWS HealthOmics allows only one reference store per account per region.
If... GetAHOReferenceStore Get details about a specific HealthOmics reference store.
AWS HealthOmics allows only one reference store per account per region.
If reference_sto... GetAHORun Get details about a specific run.
Args:
ctx: MCP context for error reporting
run_id: ID of the run to retrieve
aws_profile: Optional A... GetAHORunCache Get details of a specific HealthOmics run cache.
Args:
ctx: MCP context for error reporting
cache_id: ID of the run cache to retrieve
... GetAHORunEngineLogs Retrieve engine logs containing STDOUT and STDERR from the workflow engine process.
These logs contain all output from the workflow engine process... GetAHORunGroup Get details of a specific HealthOmics run group.
Args:
ctx: MCP context for error reporting
run_group_id: ID of the run group to retrieve
... GetAHORunLogs Retrieve high-level run logs that show workflow execution events.
These logs contain a high-level summary of events during a run including:
- Run ... GetAHORunManifestLogs Retrieve run manifest logs produced when a workflow completes or fails.
These logs contain a summary of the overall workflow including:
- Runtime ... GetAHORunTask Get details about a specific task.
Args:
ctx: MCP context for error reporting
run_id: ID of the run
task_id: ID of the task
aws_pr... GetAHOSequenceStore Get details about a specific HealthOmics sequence store.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID of the seque... GetAHOSupportedRegions Get the list of AWS regions where HealthOmics is available.
Args:
ctx: MCP context for error reporting
Returns:
Dictionary containing the... GetAHOTaskLogs Retrieve logs for a specific workflow task containing STDOUT and STDERR.
These logs contain the output from a specific task process including:
- T... GetAHOWorkflow Get details about a specific workflow.
Args:
ctx: MCP context for error reporting
workflow_id: ID of the workflow to retrieve
export_d... GetCodeConnection Get details about a specific CodeConnection.
This function retrieves detailed information about a specific AWS
CodeConnection, including its curre... GetSupportedFileTypes Get information about supported genomics file types.
Args:
ctx: MCP context for error reporting
Returns:
Dictionary containing informatio... LintAHOWorkflowBundle Lint multi-file WDL or CWL workflow bundles and return validation findings.
This tool validates multi-file workflow bundles using appropriate lint... LintAHOWorkflowDefinition Lint WDL or CWL workflow definitions and return validation findings.
This tool validates workflow definitions using appropriate linting tools:
- W... ListAHOBatches List HealthOmics batches.
Args:
ctx: MCP context for error reporting
status: Optional filter by batch status
name: Optional filter by ... ListAHOConfigurations List HealthOmics configurations.
Args:
ctx: MCP context for error reporting
max_results: Maximum number of results to return
next_toke... ListAHOReadSetExportJobs List read set export jobs for a sequence store.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID of the sequence store... ListAHOReadSetImportJobs List read set import jobs for a sequence store.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ID of the sequence store... ListAHOReadSets List read sets in a HealthOmics sequence store with optional filtering.
Args:
ctx: MCP context for error reporting
sequence_store_id: The ... ListAHOReferenceImportJobs List reference import jobs for a reference store.
AWS HealthOmics allows only one reference store per account per region.
If reference_store_id is... ListAHOReferences List references in a HealthOmics reference store with optional filtering.
AWS HealthOmics allows only one reference store per account per region.
... ListAHOReferenceStores List HealthOmics reference stores.
Args:
ctx: MCP context for error reporting
name_filter: Filter stores by name
max_results: Maximum ... ListAHORunCaches List HealthOmics run caches.
Args:
ctx: MCP context for error reporting
name: Filter by run cache name
status: Filter by run cache sta... ListAHORunGroups List HealthOmics run groups.
Args:
ctx: MCP context for error reporting
name: Filter by run group name
max_results: Maximum number of ... ListAHORuns List workflow runs.
Args:
ctx: MCP context for error reporting
max_results: Maximum number of results to return (default: 10)
next_tok... ListAHORunsInBatch List runs within a HealthOmics batch.
Args:
ctx: MCP context for error reporting
batch_id: ID of the batch
submission_status: Optional... ListAHORunTasks List tasks for a specific run.
Args:
ctx: MCP context for error reporting
run_id: ID of the run
max_results: Maximum number of results... ListAHOSequenceStores List HealthOmics sequence stores.
Args:
ctx: MCP context for error reporting
name_filter: Filter stores by name
max_results: Maximum n... ListAHOWorkflows List available HealthOmics workflows.
Args:
ctx: MCP context for error reporting
max_results: Maximum number of results to return (default... ListAHOWorkflowVersions List versions of a workflow.
Args:
ctx: MCP context for error reporting
workflow_id: ID of the workflow
max_results: Maximum number of... ListCodeConnections List available CodeConnections.
This function retrieves existing CodeConnections that can be used with
HealthOmics workflows. Connections can be f... ListECRRepositories List ECR repositories with HealthOmics accessibility status.
Lists all ECR repositories in the current region and checks each repository's
policy ... ListPullThroughCacheRules List pull-through cache rules with HealthOmics usability status.
Lists all ECR pull-through cache rules in the current region and evaluates
each r... SearchGenomicsFiles Search for genomics files across S3 buckets, HealthOmics sequence stores, and reference stores.
This tool provides intelligent search capabilities... ValidateHealthOmicsECRConfig Validate ECR configuration for HealthOmics workflows.
Performs a comprehensive validation of the ECR configuration to ensure
HealthOmics workflows... ActivateAHOReadSets Activate archived read sets in a HealthOmics sequence store.
Starts an activation job to move read sets from archive storage back to active storag... CreateAHOConfiguration Create a new HealthOmics configuration.
Args:
ctx: MCP context for error reporting
name: Configuration name (max 50 characters)
run_co... CreateAHORunCache Create a new HealthOmics run cache.
Args:
ctx: MCP context for error reporting
cache_behavior: Cache behavior (CACHE_ALWAYS or CACHE_ON_FA... CreateAHORunGroup Create a new HealthOmics run group.
Args:
ctx: MCP context for error reporting
name: Name for the run group (1-128 characters)
max_cpu... CreateAHOSequenceStore Create a new HealthOmics sequence store.
Args:
ctx: MCP context for error reporting
name: Name for the new sequence store
description:... CreateAHOWorkflow Create a new HealthOmics workflow.
Args:
ctx: MCP context for error reporting
name: Name of the workflow
definition_source: Workflow d... CreateAHOWorkflowVersion Create a new version of an existing workflow.
Args:
ctx: MCP context for error reporting
workflow_id: ID of the workflow
version_name:... CreateCodeConnection Create a new CodeConnection.
This function creates a new AWS CodeConnection for connecting to a
third-party Git provider. The connection will be c... CreateContainerRegistryMap Create a container registry map for HealthOmics workflows.
Creates a container registry map file that can be used when creating HealthOmics
workfl... CreatePullThroughCacheForHealthOmics Create a pull-through cache rule configured for HealthOmics.
Creates an ECR pull-through cache rule for the specified upstream registry
and config... GenerateAHORunTimeline Generate a Gantt-style timeline visualization for an AWS HealthOmics workflow run.
This tool creates an SVG Gantt chart showing task execution pha... GrantHealthOmicsRepositoryAccess Grant HealthOmics access to an ECR repository.
Updates the repository policy to allow the HealthOmics service principal
(omics.amazonaws.com) to p... PackageAHOWorkflow Package workflow definition files into a base64-encoded ZIP.
Args:
ctx: MCP context for error reporting
main_file_content: Content of the ... UpdateAHORunCache Update an existing HealthOmics run cache.
Args:
ctx: MCP context for error reporting
cache_id: ID of the run cache to update
cache_beh... UpdateAHORunGroup Update an existing HealthOmics run group.
Args:
ctx: MCP context for error reporting
run_group_id: ID of the run group to update
name:... UpdateAHOSequenceStore Update a HealthOmics sequence store.
Internally fetches the current ETag before performing the update to handle
optimistic concurrency control.
A... CancelAHORunBatch Cancel all runs in a HealthOmics batch.
Args:
ctx: MCP context for error reporting
batch_id: ID of the batch to cancel
aws_profile: Op... DeleteAHOBatch Delete a HealthOmics batch metadata (does not delete runs).
Args:
ctx: MCP context for error reporting
batch_id: ID of the batch to delete... DeleteAHOConfiguration Delete a HealthOmics configuration.
Args:
ctx: MCP context for error reporting
name: Configuration name
aws_profile: Optional AWS prof... DeleteAHORunBatch Delete all runs in a HealthOmics batch.
Args:
ctx: MCP context for error reporting
batch_id: ID of the batch whose runs to delete
aws_... DiagnoseAHORunFailure Provides comprehensive diagnostic information for a failed workflow run.
This function collects multiple sources of diagnostic information includi... StartAHOReadSetExportJob Start a read set export job to export read sets from a sequence store to S3.
Args:
ctx: MCP context for error reporting
sequence_store_id:... StartAHOReadSetImportJob Start a read set import job to import genomic files from S3 into a sequence store.
Args:
ctx: MCP context for error reporting
sequence_sto... StartAHOReferenceImportJob Start a reference import job to import reference files from S3 into a reference store.
AWS HealthOmics allows only one reference store per account... StartAHORun Start a workflow run.
Args:
ctx: MCP context for error reporting
workflow_id: ID of the workflow to run
role_arn: ARN of the IAM role ... StartAHORunBatch Start a new HealthOmics run batch.
Args:
ctx: MCP context for error reporting
workflow_id: ID of the workflow to run
role_arn: IAM rol... The AWS HealthOmics MCP Server MCP server exposes 73 tools across 4 categories: Read, Write, Destructive, Execute.
Use Intercept, the open-source MCP proxy. Write YAML rules for each tool — rate limits, argument validation, or deny rules — then run Intercept in front of the AWS HealthOmics MCP Server server.
AWS HealthOmics MCP Server tools are categorised as Read (47), Write (16), Destructive (4), Execute (6). Each category has a recommended default policy.
Deterministic policy on every MCP tool call. Per-identity grants. Full audit log.