#!/bin/bash -Ceuo pipefail
# Write manifest JSON file
    cat << 'EOF' > manifest.json
{"samtools":["Filler-D0001361",["Filler-D0001361.stats"],"Filler-D0000861",["Filler-D0000861.stats"],"Filler-D0000890",["Filler-D0000890.stats"],"Filler-D0002923",["Filler-D0002923.stats"],"Filler-D0002564",["Filler-D0002564.stats"],"Filler-D0003157",["Filler-D0003157.stats"],"Filler-D0002881",["Filler-D0002881.stats"],"Filler-D0003105",["Filler-D0003105.stats"],"Filler-D0001009",["Filler-D0001009.stats"],"Filler-D0003224",["Filler-D0003224.stats"],"Filler-D0001104",["Filler-D0001104.stats"],"Filler-D0003090",["Filler-D0003090.stats"],"Filler-D0002805",["Filler-D0002805.stats"],"T21-D0003322",["T21-D0003322.stats"],"Filler-D0003241",["Filler-D0003241.stats"],"Filler-D0001322",["Filler-D0001322.stats"],"Filler-D0000637",["Filler-D0000637.stats"],"T18-D0001467",["T18-D0001467.stats"],"Filler-D0001089",["Filler-D0001089.stats"],"Filler-D0000789",["Filler-D0000789.stats"],"Filler-D0002474",["Filler-D0002474.stats"],"T21-D0003376",["T21-D0003376.stats"],"Filler-D0001215",["Filler-D0001215.stats"],"Filler-D0002530",["Filler-D0002530.stats"],"Filler-D0000335",["Filler-D0000335.stats"],"Filler-D0001515",["Filler-D0001515.stats"],"Filler-D0003441",["Filler-D0003441.stats"],"Filler-D0002693",["Filler-D0002693.stats"],"T13-D0003360",["T13-D0003360.stats"],"Filler-D0000539",["Filler-D0000539.stats"],"T18-D0003255",["T18-D0003255.stats"],"Filler-D0002999",["Filler-D0002999.stats"]],"mosdepth":["Filler-D0001361",["Filler-D0001361.mosdepth.summary.txt"],"Filler-D0000861",["Filler-D0000861.mosdepth.summary.txt"],"Filler-D0000890",["Filler-D0000890.mosdepth.summary.txt"],"Filler-D0002881",["Filler-D0002881.mosdepth.summary.txt"],"Filler-D0002923",["Filler-D0002923.mosdepth.summary.txt"],"Filler-D0001104",["Filler-D0001104.mosdepth.summary.txt"],"Filler-D0002564",["Filler-D0002564.mosdepth.summary.txt"],"Filler-D0002805",["Filler-D0002805.mosdepth.summary.txt"],"Filler-D0003157",["Filler-D0003157.mosdepth.summary.txt"],"Filler-D0003241",["Filler-D0003241.mosdepth.summary.txt"],"Filler-D0003224",["Filler-D0003224.mosdepth.summary.txt"],"Filler-D0003105",["Filler-D0003105.mosdepth.summary.txt"],"Filler-D0001009",["Filler-D0001009.mosdepth.summary.txt"],"T21-D0003322",["T21-D0003322.mosdepth.summary.txt"],"Filler-D0003090",["Filler-D0003090.mosdepth.summary.txt"],"Filler-D0001322",["Filler-D0001322.mosdepth.summary.txt"],"Filler-D0000637",["Filler-D0000637.mosdepth.summary.txt"],"Filler-D0001089",["Filler-D0001089.mosdepth.summary.txt"],"Filler-D0002474",["Filler-D0002474.mosdepth.summary.txt"],"T21-D0003376",["T21-D0003376.mosdepth.summary.txt"],"Filler-D0000789",["Filler-D0000789.mosdepth.summary.txt"],"T18-D0001467",["T18-D0001467.mosdepth.summary.txt"],"Filler-D0002530",["Filler-D0002530.mosdepth.summary.txt"],"Filler-D0001215",["Filler-D0001215.mosdepth.summary.txt"],"Filler-D0000335",["Filler-D0000335.mosdepth.summary.txt"],"Filler-D0001515",["Filler-D0001515.mosdepth.summary.txt"],"Filler-D0003441",["Filler-D0003441.mosdepth.summary.txt"],"Filler-D0002693",["Filler-D0002693.mosdepth.summary.txt"],"T13-D0003360",["T13-D0003360.mosdepth.summary.txt"],"Filler-D0000539",["Filler-D0000539.mosdepth.summary.txt"],"T18-D0003255",["T18-D0003255.mosdepth.summary.txt"],"Filler-D0002999",["Filler-D0002999.mosdepth.summary.txt"]],"sentieon_insert":[],"sentieon_hs":["Filler-D0001361",["Filler-D0001361_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000861",["Filler-D0000861_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000890",["Filler-D0000890_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002881",["Filler-D0002881_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002923",["Filler-D0002923_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001104",["Filler-D0001104_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002564",["Filler-D0002564_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002805",["Filler-D0002805_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003157",["Filler-D0003157_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003241",["Filler-D0003241_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003105",["Filler-D0003105_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003224",["Filler-D0003224_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"T21-D0003322",["T21-D0003322_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001009",["Filler-D0001009_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003090",["Filler-D0003090_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001322",["Filler-D0001322_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000637",["Filler-D0000637_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002474",["Filler-D0002474_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001089",["Filler-D0001089_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000789",["Filler-D0000789_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"T21-D0003376",["T21-D0003376_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"T18-D0001467",["T18-D0001467_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002530",["Filler-D0002530_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001215",["Filler-D0001215_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000335",["Filler-D0000335_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0001515",["Filler-D0001515_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0003441",["Filler-D0003441_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002693",["Filler-D0002693_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"T13-D0003360",["T13-D0003360_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0000539",["Filler-D0000539_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"T18-D0003255",["T18-D0003255_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"],"Filler-D0002999",["Filler-D0002999_prenatal-exome-v1-targets-hg38.sentieon.hs_metrics"]],"seqtool":[]}
EOF

    cat << 'EOF' > panel_mapping.json
{"prenatal-exome-v1-targets-hg38.bed":"prenatal_exome_v1_targets"}
EOF

    # Run aggregation script (outputs single JSON)
    aggregate_qc_metrics.py \
        --mode postdedup \
        --manifest manifest.json \
        --panel-mapping panel_mapping.json \
        --files-dir . \
        --output postdedup_qc.json \
        --no-summary

cat <<-END_VERSIONS > versions.yml
"DAQ:AGGREGATE_POSTDEDUP_QC":
    python: $(python --version | sed 's/Python //g')
    aggregate_qc_metrics: 1.0.0
END_VERSIONS