debugging Smart-Seq3

    #Smart-Seq3

    if [[ "$technology" == "smartseq"* ]];then

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

        if [[ $verbose ]]; them

        if [[ $verbose ]]; then

            echo "Note: SmartSeq-3 requires additional filtering for UMIs"

        fi

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

            perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --out $crIN

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

            mv $crIN/SmartSeq3_parsed_R1.fastq ${convR1}

            mv $crIN/SmartSeq3_parsed_R2.fastq ${convR2}

            mv $crIN/SmartSeq3_parsed_I1.fastq ${convI1}

            mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}

#            mv $crIN/SmartSeq3_parsed_R1.fastq ${convR1}

#            mv $crIN/SmartSeq3_parsed_R2.fastq ${convR2}

#            mv $crIN/SmartSeq3_parsed_I1.fastq ${convI1}

#            mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}

        done

    fi

exit 0

    #converting barcodes

    echo " adjusting barcodes of R1 files"

    if [[ $barcodeadjust != 0 ]]; then