submit-workflow-safely

Submitting Workflows Safely

This skill teaches you how to verify workflow configuration and safely submit workflows to Terra.

Pre-Submission Checklist

Before submitting a workflow, verify these three things:

1. Verify Method Configuration Points to Correct WDL Version

get_method_config(workspace_namespace, workspace_name, config_namespace, config_name)

Check the methodRepoMethod section for:

• methodNamespace: The WDL repository namespace
• methodName: The workflow name
• methodVersion: The snapshot/version number

Common issue: Configuration points to an old WDL version instead of the latest.

2. Verify Entity Data is Correct

get_entities(workspace_namespace, workspace_name, entity_type)

Verify:

• Entity exists and has expected attributes
• File paths (GCS URLs) are valid
• Required attributes are populated

Caution: For large tables (100+ entities), consider whether you need all data. See the manage-context-size skill.

3. Verify Input Mappings are Configured

In the method configuration (from step 1), check:

• inputs: Maps WDL input variables to entity attributes or literal values
• outputs: Maps WDL outputs to entity attributes for storage
• rootEntityType: Must match the entity type you're submitting

Submission Patterns

Single Entity Submission

Submit a workflow for one specific entity:

submit_workflow(
    workspace_namespace="my-namespace",
    workspace_name="my-workspace",
    config_namespace="my-config-ns",
    config_name="my-workflow-config",
    entity_type="sample",
    entity_name="sample_001",
    use_callcache=True
)

Use when: Testing a workflow, debugging with a specific sample, or processing individual items.

Batch Processing with Entity Expression

Submit a workflow for multiple entities using an expression:

submit_workflow(
    workspace_namespace="my-namespace",
    workspace_name="my-workspace",
    config_namespace="my-config-ns",
    config_name="my-workflow-config",
    entity_type="sample_set",
    entity_name="my_sample_set",
    expression="this.samples",
    use_callcache=True
)