search for fastq files in output folder when using -w

				$pigzexc -c -p $threads $bcread > $outdir/$sname.barcoderead.filtered.fastq.gz

			fi

			bash $zumisdir/zUMIs-prep.sh $outdir/$sname.barcoderead.filtered.fastq.gz $outdir/$sname.cdnaread.filtered.fastq.gz $sname $outdir $zumisdir

		fi

        if [ ! -f $outdir/$sname.cdnaread.filtered.fastq.gz ] && [ -f $outdir/zUMIs_output/filtered_fastq/$sname.cdnaread.filtered.fastq.gz ]; then

          ln -s $outdir/zUMIs_output/filtered_fastq/$sname.cdnaread.filtered.fastq.gz $outdir/$sname.cdnaread.filtered.fastq.gz

        else

          echo "I do not find reads fastq file..."

        fi

			bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt

			bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc

			fi

			perl $zumisdir/fqcheck.pl $o/$sn.barcoderead.filtered.fastq.gz $o/$sn.cdnaread.filtered.fastq.gz $sn $o

		fi

    if [ ! -f $o/$sn.cdnaread.filtered.fastq.gz ] && [ -f $o/zUMIs_output/filtered_fastq/$sn.cdnaread.filtered.fastq.gz ]; then

      ln -s $o/zUMIs_output/filtered_fastq/$sn.cdnaread.filtered.fastq.gz $o/$sn.cdnaread.filtered.fastq.gz

    else

      echo "I do not find reads fastq file..."

    fi

			$starexc --genomeDir $g --runThreadN $t --readFilesCommand zcat --sjdbGTFfile $gtf --outFileNamePrefix $o/$sn. --outSAMtype BAM Unsorted --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --sjdbOverhang $rl --twopassMode Basic --readFilesIn $o/$sn.cdnaread.filtered.fastq.gz $x

			$samtoolsexc sort -n -O bam -T temp.$sn -@ $t -m 2G -o $o/$sn.aligned.sorted.bam $o/$sn.Aligned.out.bam