#!/bin/bash -Ceuo pipefail
merge_vcf_characteristics.py \
    --target HCC1395_BL.chip.harmonized.vcf.gz \
    --source HCC1395_BL.germline.harmonized.vcf.gz \
    --output HCC1395_BL.GERMLINE.merged.vcf.gz \
    --prefix GERMLINE \


tabix -p vcf HCC1395_BL.GERMLINE.merged.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE":
    merge_vcf_characteristics: $(merge_vcf_characteristics.py --version 2>&1 | grep -o 'version.*' | cut -d' ' -f2 || echo "1.0.0")
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS