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.

api/app/services/events.py

@@ -0,0 +1,31 @@
+"""Event publishing.
+
+GCP: publish a JSON message to Pub/Sub; an Argo Events sensor turns it into an Argo Workflow.
+Local: run Nextflow directly in a background task so `docker compose up` gives a working demo.
+"""
+import asyncio
+import json
+import uuid
+
+from app.config import settings
+
+
+async def publish_vcf_uploaded(job_id: uuid.UUID, vcf_uri: str) -> None:
+    message = {"job_id": str(job_id), "vcf_uri": vcf_uri}
+    if settings.pubsub_topic:
+        from google.cloud import pubsub_v1  # optional dependency, installed in the GCP image
+
+        publisher = pubsub_v1.PublisherClient()
+        publisher.publish(settings.pubsub_topic, json.dumps(message).encode())
+        return
+
+    cmd = [
+        "nextflow", "run", "/pipeline/main.nf", "-profile", "docker",
+        "--vcf", vcf_uri, "--job_id", str(job_id), "--db_url", settings.database_url,
+    ]
+    try:
+        await asyncio.create_subprocess_exec(*cmd)
+    except FileNotFoundError:
+        # Nextflow is not installed in this environment (no Java toolchain yet);
+        # leave the job queued instead of crashing the request.
+        print(f"[rarelens] nextflow not found; cannot start pipeline for job {job_id}", flush=True)