HealthOmics workflow definition requirements

Tasks must define input/output parameters, Amazon ECR container repositories, and runtime specifications such as memory or CPU allocation.

Verify that your IAM roles have the required permissions.

Declare the output files in the workflow definition. To copy intermediate run files to the output location, declare them as workflow outputs.

The input and output locations must be in the same Region as the workflow.

HealthOmics storage workflow inputs must be in ACTIVE status. HealthOmics won't import inputs with an ARCHIVED status, causing the workflow to fail. For information about Amazon S3 object inputs, see HealthOmics run inputs.

A main location of the workflow is optional if your ZIP archive contains either a single workflow definition or a file named 'main'.

Before you create a workflow from Amazon S3 or your local drive, create a zip archive of the workflow definition files and any dependencies, such as subworkflows.

We recommend that you declare Amazon ECR containers in the workflow as input parameters for validation of the Amazon ECR permissions.

/bin

Nextflow workflow definitions may include a /bin folder with executable scripts. This path has read-only plus executable access to tasks. Tasks that rely on these scripts should use a container built with the appropriate script interpreters. Best practice is to call the interpreter directly. For example:

process my_bin_task {
   ...
   script:
      """
      python3 my_python_script.py
      """
}       
        

includeConfig

Nextflow-based workflow definitions can include nextflow.config files that help to abstract parameter definitions or process resource profiles. To support development and execution of Nextflow pipelines on multiple environments, use a HealthOmics-specific configuration that you add to the global config using the includeConfig directive. To maintain portability, configure the workflow to include the file only when running on HealthOmics by using the following code:

// at the end of the nextflow.config file
if ("$AWS_WORKFLOW_RUN") {
    includeConfig 'conf/omics.config'
}       

Reports

HealthOmics doesn't support engine-generated dag, trace, and execution reports. You can generate alternatives to the trace and execution reports using a combination of GetRun and GetRunTask API calls.

Container image uri interpolation

HealthOmics allows the dockerPull property of the DockerRequirement to be an inline javascript expression. For example:

requirements:
  DockerRequirement:
    dockerPull: "$(inputs.container_image)"  

This allows you to specifying container image URIs as input parameters to the workflow.

Javascript expressions

Javascript expressions must be strict mode compliant.

Operation process

HealthOmics doesn't support CWL Operation processes.