#!/bin/bash -euo pipefail
mkdir -p merged/Reports

first=true
for f in ds*/*; do
    if [ "$first" = true ]; then
        cat "$f" > merged/Reports/Demultiplex_Stats.csv
        first=false
    else
        tail -n+2 "$f" >> merged/Reports/Demultiplex_Stats.csv
    fi
done

if ls tu*/* 1>/dev/null 2>&1; then
    first=true
    for f in tu*/*; do
        if [ "$first" = true ]; then
            cat "$f" > merged/Reports/Top_Unknown_Barcodes.csv
            first=false
        else
            tail -n+2 "$f" >> merged/Reports/Top_Unknown_Barcodes.csv
        fi
    done
fi

sample_sheet_qc.py \
    merged \
    --fail-threshold 10.0 --warning-threshold 5.0 --non-ntc-threshold 1000000 --ntc-threshold 2000000 \
    --output-dir . \
    --create-pass-file

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK":
    sample_sheet_qc: 1.1.0
END_VERSIONS