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.

infra/argo-workflows/annotate.yaml

@@ -0,0 +1,37 @@
+# Triggered by an Argo Events sensor listening on the Pub/Sub topic "vcf-uploaded".
+apiVersion: argoproj.io/v1alpha1
+kind: WorkflowTemplate
+metadata: { name: annotate-vcf, namespace: rarelens }
+spec:
+  entrypoint: nextflow
+  arguments:
+    parameters:
+      - { name: job_id }
+      - { name: vcf_uri }
+  templates:
+    - name: nextflow
+      inputs:
+        parameters: [{ name: job_id }, { name: vcf_uri }]
+      serviceAccountName: rarelens-pipeline
+      container:
+        image: europe-west2-docker.pkg.dev/PROJECT/rarelens/pipeline:latest
+        command: [nextflow]
+        args:
+          - run
+          - /pipeline/main.nf
+          - -profile
+          - gcp
+          - --vcf
+          - "{{inputs.parameters.vcf_uri}}"
+          - --job_id
+          - "{{inputs.parameters.job_id}}"
+          - --db_url
+          - "$(DATABASE_URL)"
+        envFrom: [{ secretRef: { name: api-secrets } }]
+        resources: { requests: { cpu: "2", memory: 4Gi } }
+    - name: score
+      # Optional GPU step for the deep-learning baseline; Autopilot schedules on an L4 node.
+      nodeSelector: { cloud.google.com/gke-accelerator: nvidia-l4 }
+      container:
+        image: europe-west2-docker.pkg.dev/PROJECT/rarelens/ml:latest
+        resources: { limits: { nvidia.com/gpu: 1 } }