Skip to content

Submit Workflows

Submit WDL workflows to Cromwell.

  • One Command

    Submit workflows with a single CLI command

  • Labels Support

    Organize workflows with custom labels

  • Dependencies

    Include imported WDL files via ZIP bundles

Quick Start

pumbaa workflow submit --workflow FILE [OPTIONS]

Flags

Flag Alias Required Description
--workflow -w WDL workflow file
--inputs -i Inputs JSON file
--options -o Options JSON file
--dependencies -d Dependencies ZIP file
--label -l Labels (key=value)

Examples

pumbaa workflow submit --workflow hello.wdl

pumbaa workflow submit \
  --workflow pipeline.wdl \
  --inputs inputs.json

pumbaa workflow submit \
  --workflow analysis.wdl \
  --inputs inputs.json \
  --options options.json \
  --dependencies deps.zip \
  --label sample=S001 \
  --label env=prod

Input File

JSON format matching WDL inputs:

{
  "workflow.sample_name": "SAMPLE-001",
  "workflow.fastq": "gs://bucket/sample.fastq.gz",
  "workflow.reference": "gs://bucket/ref.fa"
}

Options File

Configure workflow execution:

{
  "final_workflow_outputs_dir": "gs://bucket/outputs",
  "delete_intermediate_output_files": true,
  "write_to_cache": true,
  "read_from_cache": true
}
Option Description
final_workflow_outputs_dir Output location
delete_intermediate_output_files Cleanup intermediates
write_to_cache / read_from_cache Call caching

Dependencies

For workflows with imports, create ZIP with imported files:

pumbaa bundle create --workflow workflow.wdl --output deps.zip

Then submit:

pumbaa workflow submit --workflow workflow.wdl --dependencies deps.zip

Labels

Organize workflows with labels:

pumbaa workflow submit \
  --workflow pipeline.wdl \
  --label sample=S001 \
  --label pipeline=variant-calling \
  --label user=$USER

Filter in Dashboard

Press L in dashboard to filter by labels.

Response

{
  "id": "abc12345-6789-0def-ghij-klmnopqrstuv",
  "status": "Submitted"
}

Use the ID to monitor:

pumbaa dashboard                    # Interactive
pumbaa workflow debug <id>          # Debug view  
pumbaa workflow query --id <id>     # CLI query

See Also