#!/bin/bash -Ceuo pipefail
mkdir -p raw_vcfs/ vcfs/
cnv_pipe make-probe-merged-vcfs \
    HCC1395_BL_probe_sample.parquet \
    Homo_sapiens_assembly38.fasta \
    raw_vcfs/ \
    1 \

# cnv_pipe names the VCF after the parquet's internal sample_id. In prod
# that equals germline_control_1 (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/germline_control_1.vcf