#!/bin/bash -Ceuo pipefail
mkdir -p raw_vcfs/ vcfs/
cnv_pipe make-probe-merged-vcfs \
germline_cnv_model.parquet \
Homo_sapiens_assembly38.fasta \
raw_vcfs/ \
1 \
--panel-conf altera
# cnv_pipe names the VCF after the parquet's internal sample_id. In prod
# that equals Sig_18_Blood (autorun builds one parquet per normal sample),
# so the rename is effectively a relabel. In CI regression/edge-cases we
# reuse a single fixture parquet across many workorder rows — this rename
# gives each row a unique filename so publishDir doesn't collide.
mv raw_vcfs/*.vcf vcfs/Sig_18_Blood.vcf