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/nextflow.config

@@ -0,0 +1,24 @@
+params {
+    vcf        = null
+    job_id     = null
+    db_url     = null
+    outdir     = "results"
+    assembly   = "GRCh38"
+    vep_cache  = "${projectDir}/cache/vep"     // download once with `vep_install`; or use --offline false
+    vep_plugins = "CADD,AlphaMissense"
+}
+
+profiles {
+    docker { docker.enabled = true }
+    gcp {
+        process.executor = 'k8s'               // runs inside GKE via Argo; Nextflow k8s executor
+        workDir = "gs://${params.bucket}/work"
+        google.project = params.project
+    }
+}
+
+process {
+    withName: VEP        { container = 'ensemblorg/ensembl-vep:release_113.0'; cpus = 4; memory = '8 GB' }
+    withName: NORMALISE  { container = 'quay.io/biocontainers/bcftools:1.20--h8b25389_0' }
+    withName: LOAD_DB    { container = 'ghcr.io/lynchaos/rarelens-loader:latest' }
+}