add mock UMI for Quartz-Seq and RamDA-Seq

        done

    fi

    #Quartz-Seq and RamDA-Seq: add mock UMI for non-UMI techniques

    if [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then

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

        if [[ $verbose ]]; then

            echo "Note: ICELL8 v2 does not contain UMIs"

        fi

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

            if [[ $nonUMI ]]; then

                # 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

                #returns a combined R1 file with barcode and mock UMI

                ## 11 bp barcode, 10 bp UMI (TSO not handled yet)

                mv $crIN/mock_UMI.fastq ${convR1}

            fi

        done

    fi

    #QuartzSeq: remove adapter

    #Quartz-Seq2: remove adapter

    if [[ "$technology" == "quartz-seq2-384" ]]; then

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

        echo "  ...remove adapter for ${technology}"