#!/bin/bash -Ceuo pipefail
# Write manifest JSON file
    cat << 'EOF' > manifest.json
{"samtools":["13929215-cfDNA",["13929215-cfDNA.stats"],"14558439-cfDNA",["14558439-cfDNA.stats"],"13432478-cfDNA",["13432478-cfDNA.stats"],"14862332-cfDNA",["14862332-cfDNA.stats"],"D0000162_22q",["D0000162_22q.stats"],"16098090-cfDNA",["16098090-cfDNA.stats"],"14138939-cfDNA",["14138939-cfDNA.stats"],"14389853-cfDNA",["14389853-cfDNA.stats"],"14668865-cfDNA",["14668865-cfDNA.stats"],"15921737-cfDNA",["15921737-cfDNA.stats"],"13739430-cfDNA",["13739430-cfDNA.stats"],"10PercentHG514",["10PercentHG514.stats"],"SH032_HG513",["SH032_HG513.stats"],"40PercentNA24385",["40PercentNA24385.stats"],"5PercentHG514",["5PercentHG514.stats"],"1_25PercentNA24385",["1_25PercentNA24385.stats"],"13511611-cfDNA",["13511611-cfDNA.stats"],"40PercentHG514",["40PercentHG514.stats"],"15451964-cfDNA",["15451964-cfDNA.stats"],"D0001109_22q",["D0001109_22q.stats"],"SH032_HG514",["SH032_HG514.stats"],"2_5PercentNA24385",["2_5PercentNA24385.stats"],"20PercentHG514",["20PercentHG514.stats"],"3140_NA24143",["3140_NA24143.stats"],"D0001483_22q",["D0001483_22q.stats"],"D0000476_22q",["D0000476_22q.stats"],"20PercentNA24385",["20PercentNA24385.stats"],"10PercentNA24385",["10PercentNA24385.stats"],"1_25PercentHG514",["1_25PercentHG514.stats"],"5PercentNA24385",["5PercentNA24385.stats"],"2_5PercentHG514",["2_5PercentHG514.stats"],"3140_NA24385",["3140_NA24385.stats"]],"mosdepth":["13929215-cfDNA",["13929215-cfDNA.mosdepth.summary.txt"],"14558439-cfDNA",["14558439-cfDNA.mosdepth.summary.txt"],"14862332-cfDNA",["14862332-cfDNA.mosdepth.summary.txt"],"D0000162_22q",["D0000162_22q.mosdepth.summary.txt"],"13432478-cfDNA",["13432478-cfDNA.mosdepth.summary.txt"],"16098090-cfDNA",["16098090-cfDNA.mosdepth.summary.txt"],"14138939-cfDNA",["14138939-cfDNA.mosdepth.summary.txt"],"14389853-cfDNA",["14389853-cfDNA.mosdepth.summary.txt"],"14668865-cfDNA",["14668865-cfDNA.mosdepth.summary.txt"],"13739430-cfDNA",["13739430-cfDNA.mosdepth.summary.txt"],"15921737-cfDNA",["15921737-cfDNA.mosdepth.summary.txt"],"10PercentHG514",["10PercentHG514.mosdepth.summary.txt"],"40PercentNA24385",["40PercentNA24385.mosdepth.summary.txt"],"SH032_HG513",["SH032_HG513.mosdepth.summary.txt"],"5PercentHG514",["5PercentHG514.mosdepth.summary.txt"],"1_25PercentNA24385",["1_25PercentNA24385.mosdepth.summary.txt"],"13511611-cfDNA",["13511611-cfDNA.mosdepth.summary.txt"],"D0001109_22q",["D0001109_22q.mosdepth.summary.txt"],"15451964-cfDNA",["15451964-cfDNA.mosdepth.summary.txt"],"40PercentHG514",["40PercentHG514.mosdepth.summary.txt"],"SH032_HG514",["SH032_HG514.mosdepth.summary.txt"],"2_5PercentNA24385",["2_5PercentNA24385.mosdepth.summary.txt"],"20PercentHG514",["20PercentHG514.mosdepth.summary.txt"],"D0001483_22q",["D0001483_22q.mosdepth.summary.txt"],"D0000476_22q",["D0000476_22q.mosdepth.summary.txt"],"3140_NA24143",["3140_NA24143.mosdepth.summary.txt"],"20PercentNA24385",["20PercentNA24385.mosdepth.summary.txt"],"1_25PercentHG514",["1_25PercentHG514.mosdepth.summary.txt"],"10PercentNA24385",["10PercentNA24385.mosdepth.summary.txt"],"5PercentNA24385",["5PercentNA24385.mosdepth.summary.txt"],"2_5PercentHG514",["2_5PercentHG514.mosdepth.summary.txt"],"3140_NA24385",["3140_NA24385.mosdepth.summary.txt"]],"sentieon_insert":[],"sentieon_hs":["13929215-cfDNA",["13929215-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"14558439-cfDNA",["14558439-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"13432478-cfDNA",["13432478-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"D0000162_22q",["D0000162_22q_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"14862332-cfDNA",["14862332-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"16098090-cfDNA",["16098090-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"14138939-cfDNA",["14138939-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"14668865-cfDNA",["14668865-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"14389853-cfDNA",["14389853-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"15921737-cfDNA",["15921737-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"13739430-cfDNA",["13739430-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"10PercentHG514",["10PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"40PercentNA24385",["40PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"SH032_HG513",["SH032_HG513_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"5PercentHG514",["5PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"1_25PercentNA24385",["1_25PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"13511611-cfDNA",["13511611-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"D0001109_22q",["D0001109_22q_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"15451964-cfDNA",["15451964-cfDNA_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"40PercentHG514",["40PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"SH032_HG514",["SH032_HG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"2_5PercentNA24385",["2_5PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"D0001483_22q",["D0001483_22q_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"20PercentHG514",["20PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"D0000476_22q",["D0000476_22q_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"20PercentNA24385",["20PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"3140_NA24143",["3140_NA24143_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"10PercentNA24385",["10PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"5PercentNA24385",["5PercentNA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"1_25PercentHG514",["1_25PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"2_5PercentHG514",["2_5PercentHG514_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"],"3140_NA24385",["3140_NA24385_IDT.Exomev2.targets.hg38.sentieon.hs_metrics"]],"seqtool":[]}
EOF

    cat << 'EOF' > panel_mapping.json
{"IDT.Exomev2.targets.hg38.bed":"idt_exome_v2_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