Sapporo WES — Quick Reference¶

Endpoint: export SAPPORO_ENDPOINT=http://localhost:1122

1. Check service¶

curl -s $SAPPORO_ENDPOINT/service-info | jq '{engines: .workflow_engine_versions, types: .workflow_type_versions}'

2. Submit¶

RUN_ID=$(curl -s -X POST $SAPPORO_ENDPOINT/runs \
  -H "Content-Type: application/json" \
  -d '{
    "workflow_type": "CWL",
    "workflow_type_version": "v1.0",
    "workflow_url": "https://example.com/workflow.cwl",
    "workflow_engine": "cwltool",
    "workflow_params": {"input": "https://example.com/data.txt"}
  }' | jq -r .run_id)

Required fields: workflow_type, workflow_type_version, workflow_url, workflow_engine.

3. Poll¶

curl -s $SAPPORO_ENDPOINT/runs/$RUN_ID/status | jq -r .state
# QUEUED → INITIALIZING → RUNNING → COMPLETE | EXECUTOR_ERROR | SYSTEM_ERROR

4. Outputs¶

curl -s $SAPPORO_ENDPOINT/runs/$RUN_ID/outputs | jq .outputs          # list
curl -s -o out.zip "$SAPPORO_ENDPOINT/runs/$RUN_ID/outputs?download=true"  # zip
curl -s -o file.txt "$SAPPORO_ENDPOINT/runs/$RUN_ID/outputs/file.txt"      # single file

On error¶

curl -s $SAPPORO_ENDPOINT/runs/$RUN_ID | jq '{exit_code: .run_log.exit_code, stderr: .run_log.stderr}'

Engine / type table¶

Engine	Type	Version
`cwltool`	`CWL`	`v1.0`, `v1.2`
`cromwell`	`WDL`	`1.0`
`nextflow`	`NFL`	`DSL2`
`snakemake`	`SMK`	`v1`

Full reference: docs/agent-skill.md