enable skipping conversion

        fi

        bash $(basename "$0") -t $technology --setup

        setup=false

        if [ ! convert ]

            then

            echo "  warning: technology changed to $technology since last run"

            convert=true

        fi

    fi

else    

        echo " using setup $technology from previous whitelist configuration ..."

LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//')

if [ convert ]

then

#create directory of modified files

echo "    creating a folder for all cellranger input files..."

crIN="cellranger"

    done

    echo "    conversion complete"

fi

#close conversion

fi

#running cellranger

echo "    running cellranger..."

    j="--jobmode=$jobmode"

fi

start=`date +%s`

echo "cellranger count --id=$id \

        --fastqs=$crIN \

        --lanes=$LANE \

        --r1-length="26" \

        --chemistry=$chemistry \

        --transcriptome=$reference \

        --sample=$SAMPLE \

        $d \

        $n \

        $j

"

cellranger count --id=$id \

        --fastqs=$crIN \

        --lanes=$LANE \