refactor cloupe preprocess suppression

    elif [[ $lastcall_p == "default:10x" ]] || [[ ! -f $lastcallfile ]]; then

        #disable cloupe generation

        if [[ $verbose  ]]; then

           echo "diasble cloupe"

            echo "disable cloupe"

        fi

#        sed -i '/output_for_cloupe/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

#        sed -i '/out cloupe cloupe/ {s/^#*#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro #

        sed -i 's/@include "_cloupe_stages.mro"/#@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

        ## list cloupe output as null

        sed -i '/output_for_cloupe/s/CLOUPE_PREPROCESS\.output_for_cloupe/null/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

        sed -i '/output_for_cloupe/s/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

        ## remove cloupe from outputs

        sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

#remove 11 lines for cloupe preprocess call

        #remove 11 lines for cloupe preprocess call (all folowing steps are needed to be suppressed together or call will break)

        ## remove defining CLOUPE_PREPROCESS

        sed -i 's/@include "_cloupe_stages.mro"/#@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

        ## remove listing CLOUPE in output

        sed -i '/output_for_cloupe/s/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

        ## remove calling CLOUPE_PREPROCESS

        ### iterate over all files calling CLOUPE_PREPROCESS

        for file in $(grep -l  "call CLOUPE_PREPROCES"  /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/mro/*.mro )

        do

            #find  start of CLOUPE_PREPROCESS call

            num=$(grep -n "call CLOUPE_PREPROCESS" $file |  head -n 1 | cut -d":" -f1)

            #find end of CLOUPE_PREPROCESS call

            num2=$(($num +$(tail -n $(echo $(($(wc -l $file | cut -f1 -d " ") - $num))) $file | grep -n ")" | head -n 1 | cut -d":" -f1)))

            if [[ $verbose ]]; then

               echo "lines ${num}-${num2} commented out of $file"

            fi

            eval "sed -i '$(echo "${num},${num2}s/^/#/g")' $file"

        done

    fi

    echo " ${cellrangerpath} set for $technology"