add subroutine for ICELL8 v2 (non-UMI)

        done

    fi

    #ICELL8 version 2 (non-UMI technology)

    if [[ "$technology" == "icell8" ]] && [[ $nonUMI ]];;then

        echo "  ...processsing for ${technology}"

        if [[ $verbose ]]; then

            echo "Note: ICELL8 v2 does not contain UMIs"

        fi

        for convFile in "${convFiles[@]}"; do

            read=$convFile

            convR1=$read

            convR2=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

            if [[ $chemistry == "SC5P"* ]] || [[ $chemistry == "five"* ]]; then

                ## echo " ...remove internal reads for ${technology} by matching TSO sequence for UMI reads"

                # filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters 

                perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --tag="AAAAAAAAAAAAAAAAAAAA" --out_dir $crIN

                echo "  ...trim tag sequence from R1"

                # returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2

                mv $crIN/parsed_R1.fastq ${convR1}

                mv $crIN/parsed_R2.fastq ${convR2}

                mv $crIN/parsed_I1.fastq ${convI1}

                mv $crIN/parsed_I2.fastq ${convI2}

            fi

            # add mock UMI (count reads instead of UMI) barcodelength=16, umi_default=10

            perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default

            umilength=$umi_default

            umiadjust=0

            chemistry="SC3Pv2"

            #returns a combined R1 file with barcode and mock UMI

            ## 16 bp barcode, 10 bp UMI, GGG for TSO

            mv $crIN/mock_UMI.fastq ${convR1}

            if [[ $chemistry == "SC5P"* ]] || [[ $chemistry == "five"* ]]; then

                #convert TSO to expected length for 10x 5' (TSS in R1 from base 39)

                echo " handling $convFile ..."

                tsoS="TTTCTTATATGGG" #<- confirm tag sequence with Takara reps

                tsoQ="IIIIIIIIIIIII"

                #Add 10x TSO characters to the end of the sequence

                cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')

                if [[ $verbose ]]; then

                    echo technology $technology

                    echo barcode: $barcodelength

                    echo umi: $umilength

                    echo $cmd

                fi

                # run command with barcode and umi length, e.g.,: sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp

                eval $cmd

                mv ${crIN}/.temp $convFile

                #Add n characters to the end of the quality

                cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')

                # run command with barcode and umi length, e.g.,: sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp

                eval $cmd

                mv ${crIN}/.temp $convFile

            fi

            echo "  ${convFile} adjusted"

       done

    fi

    #inDrops: remove adapter (see links below for details)

    ## https://github.com/BUStools/bustools/issues/4

    ## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html