#!/bin/bash -euo pipefail
manta_sv_normalize.py \
    --input 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz \
    --sample-id 1136_85O-T1-TDNA-1_A23WJ5GLT4_8 \
    --prefix 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz \
    --output-dir .

# Copy the original VCF with standardized name for publishing
cp 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.vcf.gz

# Copy index if it exists
if [ -f "1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz.tbi" ]; then
    cp 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz.tbi 1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.vcf.gz.tbi
fi

cat <<-END_VERSIONS > versions.yml
"NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE":
    python: $(python --version | sed 's/Python //')
    manta_sv_normalize: "1.0.0"
END_VERSIONS