restore checks for detect chemistry and debug

        done

    fi

    #check for custom whitelist

    if [[ $custombarcodes ]]; then

    if [[ $custombarcodes == "true" ]]; then

        #disable detect chemistry check for custom whitelist

        sed -i "s/ raise NoChemistryFoundException/ return best_chem \#raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ (100\.0 \* best_frac/ \#(100\.0 \* best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        if [[ $verbose ]]; then

            echo "disable detect chemistry check..."

        fi

        sed -i "s/ raise NoChemistryFoundException/ return best_chem #raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ (100\.0 \* best_frac/ #(100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    else

         if [[ $verbose ]]; then

             echo "restore detect chemistry check..."

        fi

        #restore detect chemistry check for custom whitelist

        sed -i "s/ return best_chem \#raise NoChemistryFoundException/ raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ \#(100\.0 \* best_frac/ (100\.0 \* best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

        sed -i "s/ \#(100\.0 \* best_frac/ (100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

    fi

    echo " ${cellrangerpath} set for $technology"