Workflow linters in HealthOmics - AWS HealthOmics

Workflow linters in HealthOmics

After you create a workflow, we recommend that you run a linter on the workflow before you start the first run. The linter detects errors that can cause the run to fail.

For WDL, HealthOmics automatically runs a linter when you create the workflow. The linter output is available in the statusMessage field of the get-workflow response. Use the following CLI command to retrieve the status output (use the workflow ID of the WDL workflow that you created): 

aws omics get-workflow 
   —id 123456 
   —query 'statusMessage'

HealthOmics provides linters that you can run on the workflow defnition before you create the workflow. Run these linters on existing pipelines that you're migrating to HealthOmics.

  • WDL – A public Amazon ECR image to run a WDL linter.

  • Nextflow – A public Amazon ECR image to run Linter rules for Nextflow. You can access the source code for this linter from GitHub.

  • CWL – not available