Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

README.md

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+# rarelens
+
+A small, end-to-end variant interpretation platform for rare genetic disease research.
+Scientists upload a VCF, a Nextflow workflow annotates it with Ensembl VEP, a machine
+learning model scores each variant, and results are browsable in a web app.
+
+This repository is a **self-training lab**. It exists so that one engineer can learn, in
+public, how a modern life-sciences platform is built end to end: full-stack application,
+scientific pipeline, ML serving, and cloud infrastructure, all in one monorepo. It is not a
+clinical tool and makes no diagnostic claims.
+
+## What is in the box
+
+| Layer      | Technology                                             | Directory            |
+|------------|--------------------------------------------------------|----------------------|
+| Pipeline   | Nextflow DSL2, bcftools, Ensembl VEP, Docker           | `pipeline/`          |
+| API        | FastAPI, Pydantic v2, SQLAlchemy 2.0 (async), Alembic  | `api/`               |
+| Database   | PostgreSQL 16                                          | `docker-compose.yml` |
+| Frontend   | SvelteKit, TypeScript                                  | `web/`               |
+| ML         | LightGBM pathogenicity scorer, MLflow tracking         | `ml/`                |
+| Orchestration | Argo Workflows (pipeline), Pub/Sub (events)         | `infra/argo-workflows/` |
+| Platform   | Kubernetes (Kustomize), ArgoCD (GitOps)                | `infra/k8s/`, `infra/argocd/` |
+| Cloud      | GCP: GKE Autopilot, Cloud SQL, GCS, Artifact Registry  | `infra/terraform/`   |
+| CI/CD      | GitHub Actions, Workload Identity Federation           | `.github/workflows/` |
+
+## Quick start (local)
+
+```bash
+make up          # postgres + api + web via docker-compose
+make migrate     # alembic upgrade head
+make pipeline    # nextflow run pipeline/main.nf -profile docker --vcf data/example.vcf.gz
+make kind        # spin up a local kind cluster and apply infra/k8s/overlays/local
+```
+
+Then open http://localhost:5173.
+
+## Architecture
+
+See [docs/architecture.md](docs/architecture.md) for the diagram and the reasoning behind
+each choice.
+
+## Status
+
+Work in progress. Milestones, in order:
+
+1. Skeleton, Postgres, FastAPI, Nextflow VEP annotation on a public VCF, CI green
+2. SvelteKit UI: sample list, variant table with filters, job status
+3. Kubernetes manifests, kind, Argo Workflows trigger
+4. Terraform for GCP, ArgoCD GitOps deploy
+5. Pathogenicity model, MLflow registry, prediction endpoint
+
+## Licence
+
+AGPL-3.0. Test data are public (ClinVar, gnomAD subsets); no patient data are used or accepted.