CWL workflow definition specifics - AWS HealthOmics

AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.

CWL workflow definition specifics

Workflows written in Common Workflow Language, or CWL, offer similar functionality to workflows written in WDL and Nextflow. You can use Amazon S3 or HealthOmics storage URIs as input parameters.

If you define input in a secondaryFile in a sub workflow, add the same definition in the main workflow.

HealthOmics workflows don't support operation processes. To learn more about operations processes in CWL workflows, see the CWL documentation.

To convert an existing CWL workflow definition file to use HealthOmics, make the following changes:

  • Replace all Docker container URIs with Amazon ECR URIs.

  • Make sure that all the workflow files are declared in the main workflow as input, and all variables are explicitly defined.

  • Make sure that all JavaScript code is strict-mode complaint.

CWL workflows should be defined for each container used. It isn't recommended to hardcode the dockerPull entry with a fixed Amazon ECR URI.

The following is an example of a workflow written in CWL. 


cwlVersion: v1.2
class: Workflow

inputs:
in_file:
type: File
secondaryFiles: [.fai]

out_filename: string
docker_image: string


outputs:
copied_file:
type: File
outputSource: copy_step/copied_file

steps:
copy_step:
in:
  in_file: in_file
  out_filename: out_filename
  docker_image: docker_image
out: [copied_file]
run: copy.cwl

The following file defines the copy.cwl task.


cwlVersion: v1.2
class: CommandLineTool
baseCommand: cp

inputs:
in_file:
type: File
secondaryFiles: [.fai]
inputBinding:
  position: 1

out_filename:
type: string
inputBinding:
  position: 2
docker_image:
type: string

outputs:
copied_file:
type: File
outputBinding:
    glob: $(inputs.out_filename)

requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: "$(inputs.docker_image)"

The following is an example of a workflow written in CWL with a GPU requirement.

cwlVersion: v1.2
class: CommandLineTool
baseCommand: ["/bin/bash", "docm_haplotypeCaller.sh"]
$namespaces:
cwltool: http://commonwl.org/cwltool#
requirements:
cwltool:CUDARequirement:
cudaDeviceCountMin: 1
cudaComputeCapability: "nvidia-tesla-t4" 
cudaVersionMin: "1.0"
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing:
- entryname: 'docm_haplotypeCaller.sh'
  entry: |
          nvidia-smi --query-gpu=gpu_name,gpu_bus_id,vbios_version --format=csv   

inputs: []
outputs: []