DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega01"

mkdir -p $DELIVERY_FOLDER/assembly

# Assembly service
cd $DELIVERY_FOLDER/assembly

# Links to reports
ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/multiqc/multiqc_report.html .
ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/summary_assembly_metrics_mqc.csv .
ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/kmerfinder_summary.csv .
ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/global_report/report.html quast_global_report.html

# Links to per reference reports
for dir in ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/per_reference_reports/*; do
    base=$(basename "$dir")
    if compgen -G "$dir" > /dev/null; then
        ln -s "$dir/report.html" "quast_${base}_report.html"
    fi
done

# Links to assemblies
assembly_dirs=(unicycler dragonflye canu miniasm)
for tool in "${assembly_dirs[@]}"; do
    path="../../../ANALYSIS/*ASSEMBLY/03-assembly/${tool}"
    if compgen -G "$path" > /dev/null; then
        find $path -type d -exec ln -nsf {} assemblies \;
        break
    fi
done
cd -
