#!/bin/bash -Ceuo pipefail
multiqc \
    --force \
    --title "REGRESSION" \
    --cl-config '{"intro_text":"MultiQC Report for DAQ. Includes data from all the QC tools in DAQ.","seqtool_panels":[{"name":"all_targets","bed":"xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed"},{"name":"all_probes","bed":"xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed"},{"name":"boosted_depth","bed":"altera_v3_targets_postQC_hg38.bed"},{"name":"coding_depth","bed":"altera_v3_targets_coding_postQC_hg38.bed"},{"name":"noncoding_depth","bed":"altera_v3_targets_noncoding_postQC_hg38.bed"},{"name":"non_boosted_depth","bed":"xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed"},{"name":"hotspot_depth","bed":"FINAL_hotspot_list_07302025_hg38_sorted.bed"},{"name":"foresight_depth","bed":"foresight_clarity_targets_hg38.bed"}],"extra_fn_clean_exts":[".md"],"section_comments":{"bclconvert":"Demultiplexing statistics from BCL Convert, run per lane","fastp":"Pre-alignment QC and adapter trimming, run per sample","samtools-stats":"Alignment statistics from samtools stats on post-dedup BAMs","picard-alignmentsummary":"Alignment summary metrics from Sentieon (Picard format)","picard-insertsize":"Insert size distribution from Sentieon (Picard format)","picard_hsmetrics":"Hybrid selection metrics from Sentieon (Picard format)","picard-markduplicates":"Duplicate marking metrics from Sentieon MarkDuplicates"}}' \
     \
    .

cat <<-END_VERSIONS > versions.yml
"DAQ:MULTIQC":
    multiqc: $(multiqc --version | sed -e "s/multiqc, version //g")
END_VERSIONS