llms.txt

# sapporo-service

> GA4GH WES implementation for running bioinformatics workflows (CWL, WDL, Nextflow, Snakemake) via REST API. Each workflow engine runs in its own Docker container.

## Agent use

- [Agent Skill](docs/agent-skill.md): Full LLM-friendly reference — submit, poll, retrieve outputs, handle errors
- [Quick Reference](docs/agent-quick-ref.md): Minimal cheat sheet for tight context budgets

## Documentation

- [Getting Started](docs/getting-started.md): Start the service, submit a workflow, retrieve results
- [Configuration](docs/configuration.md): CLI options, environment variables, executable workflows
- [Authentication](docs/authentication.md): JWT authentication
- [WES Compatibility](docs/wes-compatibility.md): Differences from GA4GH WES 1.1.0
- [Architecture](docs/architecture.md): run.sh abstraction, run directory layout, RO-Crate
- [RO-Crate](docs/ro-crate.md): Provenance metadata format

## API

- [OpenAPI spec (YAML)](openapi/sapporo-wes-spec-2.1.0.yml)
- Interactive docs available at `http://localhost:1122/docs` when the service is running