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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]

Alias: pumbaa wf s

Never written an inputs file for this workflow?

Scaffold one from the WDL instead of starting from a blank file. Submit also checks the workflow and its inputs before sending anything, so mistakes surface in seconds rather than minutes.

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
--describe -D What the run is for, kept in the local history
--label -l Labels (key=value)
--skip-preflight Submit without checking the workflow and inputs first

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 \
  --describe "reprocessing after the reference panel was rebuilt" \
  --label sample=S001 \
  --label env=prod

Say what the run is for

--describe attaches a sentence to the submission. It is kept on this machine, not sent to Cromwell — labels there are constrained and meant to be tags — and it is what makes a run recognisable weeks later in pumbaa history and in the dashboard.

Input File

JSON format matching WDL inputs — generate a template with workflow scaffold:

{
  "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 --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

✓ Workflow submitted successfully!
  Workflow ID: abc12345-6789-0def-ghij-klmnopqrstuv
  Status: Submitted

Use the ID to monitor:

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

See Also