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/modules/normalise.nf

@@ -0,0 +1,11 @@
+process NORMALISE {
+    tag "$vcf.simpleName"
+    input:  path vcf
+    output: path "${vcf.simpleName}.norm.vcf.gz", emit: vcf
+
+    script:
+    """
+    bcftools norm -m -both -Oz -o ${vcf.simpleName}.norm.vcf.gz $vcf
+    bcftools index -t ${vcf.simpleName}.norm.vcf.gz
+    """
+}