#!/bin/bash -Ceuo pipefail
# Write manifest JSON file
    cat << 'EOF' > manifest.json
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T4_1",["FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_253-T1-TDNA-1_A23MHWWLT4_1",["1136_253-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"659_cfy-T1-TDNA-1_A23MHWWLT4_1",["659_cfy-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_86S-T1-TDNA-1_A23MHWWLT4_1",["1136_86S-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1029_FRC-T1-TDNA-1_A23MHWWLT4_1",["1029_FRC-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_3MV-T1-TDNA-1_A23MHWWLT4_1",["1136_3MV-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1029_HTI-T1-TDNA-1_A23MHWWLT4_1",["1029_HTI-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_00H-T1-TDNA-1_A23MHWWLT4_1",["1136_00H-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_7GC-T1-TDNA-1_A23MHWWLT4_1",["1136_7GC-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1029_T05-T1-TDNA-1_A23MHWWLT4_1",["1029_T05-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_3LU-T1-TDNA-1_A23MHWWLT4_1",["1136_3LU-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1029_I9B-T1-TDNA-1_A23MHWWLT4_1",["1029_I9B-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"659_cVw-T1-TDNA-1_A23MHWWLT4_1",["659_cVw-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"659_bR4-T1-TDNA-1_A23MHWWLT4_1",["659_bR4-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_5TB-T1-TDNA-1_A23MHWWLT4_1",["1136_5TB-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_3U6-T1-TDNA-1_A23MHWWLT4_1",["1136_3U6-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1029_N5D-T1-TDNA-1_A23MHWWLT4_1",["1029_N5D-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_27F-T1-TDNA-1_A23MHWWLT4_1",["1136_27F-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1136_4Z5-T1-TDNA-1_A23MHWWLT4_1",["1136_4Z5-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"],"1047_JG-T1-TDNA-1_A23MHWWLT4_1",["1047_JG-T1-TDNA-1_A23MHWWLT4_1_full_basic_stats.tsv"]]}
EOF

    cat << 'EOF' > panel_mapping.json
{"xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed":"all_targets","xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed":"all_probes","altera_v3_targets_postQC_hg38.bed":"boosted_depth","altera_v3_targets_coding_postQC_hg38.bed":"coding_depth","altera_v3_targets_noncoding_postQC_hg38.bed":"noncoding_depth","xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed":"non_boosted_depth","FINAL_hotspot_list_07302025_hg38_sorted.bed":"hotspot_depth","foresight_clarity_targets_hg38.bed":"foresight_depth"}
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