sapporo 2.2.5

The sapporo-service is a standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.

sapporo-service

The sapporo-service is a standard implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification. WES provides a standardized way to submit, monitor, and retrieve results from computational workflows across different platforms.

The service builds on GA4GH WES 1.1.0 with additional capabilities defined in the sapporo-wes-2.1.0 specification, including output file downloads, RO-Crate metadata generation, run deletion, and JWT authentication. Each workflow engine runs inside its own Docker container, so the service does not require any engine-specific installation.

Supported Workflow Engines

• cwltool
• nextflow
• Toil
• cromwell
• snakemake
• ep3
• StreamFlow

Quick Start

docker compose up -d
curl localhost:1122/service-info

See the Getting Started guide for a complete walkthrough including workflow submission.

Documentation

Full documentation is available at https://sapporo-wes.github.io/sapporo-service/.

• Getting Started - First-time tutorial: start the service, submit a workflow, retrieve results
• Installation - Install with pip or Docker, volume mount configuration
• Configuration - CLI options, environment variables, executable workflows
• WES Compatibility - GA4GH WES 1.1.0 and sapporo-wes 2.x compatibility matrix
• Authentication - JWT authentication, sapporo/external mode
• Architecture - run.sh abstraction, run directory, SQLite, RO-Crate, code structure
• RO-Crate - RO-Crate metadata generation specification
• Development - Development environment, testing, release process
• Agent Skill - LLM/agent reference: submit workflows, poll status, retrieve outputs via curl
• Agent Quick Reference - Essential 4 commands in ~40 lines

License

This project is licensed under the Apache-2.0 license. See the LICENSE file for details.