#!/bin/bash -euo pipefail
manta_sv_normalize.py \
    --input FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz \
    --sample-id FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1 \
    --prefix FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz \
    --output-dir .

# Copy the original VCF with standardized name for publishing
cp FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz.vcf.gz

# Copy index if it exists
if [ -f "FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz.tbi" ]; then
    cp FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz.tbi FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_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