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.

pipeline/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { NORMALISE } from './modules/normalise'
+include { VEP }       from './modules/vep'
+include { LOAD_DB }   from './modules/load_db'
+
+workflow {
+    if (!params.vcf) error "Provide --vcf"
+    vcf_ch = Channel.fromPath(params.vcf, checkIfExists: true)
+
+    NORMALISE(vcf_ch)
+    VEP(NORMALISE.out.vcf)
+    LOAD_DB(VEP.out.tsv, params.job_id ?: 'local', params.db_url ?: 'none')
+}