senju

Genomic Data Processing & Variant Analysis Platform

Quick start

• Copy env template: cp .env.example .env
• Start local stack: docker compose up -d --build
• View setup and verification: docs/setup.md

HTTP API (skeleton)

• Backend standards: docs/backend-engineering.md (Uber style guide, linting, tests, concurrency)
• Stack: Go + Gin, REST, OpenAPI (docs/adr/0004-http-api-framework.md)
• GET /health/live — liveness
• GET /health/ready — readiness (Postgres, ClickHouse, MinIO, NATS — aligned with ADRs and the platform proposal)
• GET /version — JSON build metadata
• OpenAPI: backend/openapi/openapi.yaml

Engineering governance

• Contribution standards: docs/contributing.md
• Security baseline (JWT/RBAC, secret rotation, CI scanning): docs/security.md
• Reliability controls (checkpoint/restart, recovery assumptions): docs/reliability.md
• Performance qualification and regression gates: docs/performance.md
• PR template: .github/pull_request_template.md
• Issue templates: .github/ISSUE_TEMPLATE/
• Code ownership: CODEOWNERS

Frontend (UI Foundation)

• App location: frontend/ (Next.js App Router + React + TypeScript strict + pnpm)
• Frontend quick start:
  • docker compose up -d --build frontend api
  • open http://localhost:3001 (or FRONTEND_PORT)
  • docker compose run --rm frontend pnpm lint
  • docker compose run --rm frontend pnpm typecheck
  • docker compose run --rm frontend pnpm test
  • docker compose run --rm frontend pnpm test:contrast
  • docker compose run --rm frontend pnpm build
• Frontend engineering docs: docs/frontend/README.md
• Design principles: docs/frontend/design-principles.md
• Design system and tokens: docs/frontend/design-system.md
• Color palette: docs/frontend/color-palette.md
• Information architecture: docs/frontend/information-architecture.md
• Accessibility (WCAG 2.1 AA baseline): docs/frontend/accessibility.md
• Component standards: docs/frontend/component-standards.md
• IP guardrails for UX references: docs/frontend/ip-and-references.md
• Phase roadmap: docs/frontend/roadmap.md

Architecture decisions

• ADR index: docs/adr/README.md
• Current accepted decisions:
  • docs/adr/0001-queue-system-strategy.md
  • docs/adr/0002-database-split-postgres-clickhouse.md
  • docs/adr/0003-workflow-orchestration-strategy.md
  • docs/adr/0005-frontend-framework.md
  • docs/adr/0006-frontend-design-system.md
  • docs/adr/0007-frontend-repo-layout.md

Pipeline queue

• NATS/JetStream queue package with retry + dead-letter semantics: docs/pipeline/nats-queue.md
• FastQC worker stage implementation: backend/internal/pipeline/fastqc
• BWA + SAMtools alignment worker stage implementation: backend/internal/pipeline/alignment
• GATK variant-calling worker stage implementation: backend/internal/pipeline/gatk
• Observability baseline (Prometheus, Loki, Grafana dashboard): docs/observability.md

Variant analytics storage

• ClickHouse variant schema and VCF ingestion loader: docs/data/variants.md
• Variant query API with filters and pagination: docs/api/variant-query.md
• Pipeline orchestration API (create/run/status/outputs): docs/api/orchestration.md
• ML impact baseline API (train/predict/persistence): docs/api/ml-impact.md