add subroutine for matching Smart-Seq3 UMI

        done

    fi

    #Smart-Seq3

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

        R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

        # reads matching adapter sequence for R1

        grep -A 2 -B 1 ATTGCGCAATG test_R1.fastq  | sed '/--/d' > test_R1_umi.fastq

        #match R2 to R1 containing UMI

        fastq_pair  test_R1_umi.fastq test_R2.fastq

        # uses bbduk (decontamination using k=mers) from BBMap(BBTools) vesion 38.87

        # step 1: process as paired ends to match k-mers (adapters matched are filtered)

        bbduk.sh in1=test_R1.fastq in2=test_R2.fastq outu1=clean_R1.fq outu2=clean_R2.fq outm1=fail_R2.fastq outm2=fail_R1.fastq outs=pass_singletons.fq literal=ATTGCGCAATG k=10

        # step 2: take matched (adapter filtered) reads and remove adapter (and all bases to the left)

        bbduk.sh in1=fail_R1.fq in2=fail_R2.fq out1=trimmed_R1.fq out2=trimmed_R2.fq literal=ATTGCGCAATG ktrim=l k=11

       # match indexes to R1

       fastq_pair  test_R1_umi.fastq test_I1.fastq

       fastq_pair  test_R1_umi.fastq test_I2.fastq

       #replace original files

       mv test_I1.fastq.paired.fq test_I1.fastq

       mv test_I2.fastq.paired.fq test_I2.fastq

       mv trimmed_R1.fq test_R1.fastq

       mv trimmed_R2.fq test_R2.fastq

       rm *fastq.paired.fq *fastq.single.fq clean_R1.fq clean_R2.fq fail_R1.fastq fail_R2.fastq pass_singletons.fq  test_R1_umi.fastq

    fi

    #converting barcodes

    echo " adjusting barcodes of R1 files"

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