fix passing R2 to cellranger call

    to=`basename $fq`

    to="${crIN}/${to}"

    to=$(echo "$to" | sed 's/\.gz$//')

    crR1s+=($fq)

    crR2s+=($fq)

    if [[ $fq == *'.gz' ]]; then

        echo "    unzipping and redirecting $fq file..."

        echo "        handling $fq"

        if [[ "$technology" == "nadia" ]]; then

            echo "        converting barcodes of"

            sed -i '2~4s/^/AAAA/' $fq #Add AAAA to every read

            sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read

            echo "        converting quality scores"

            sed -i '4~4s/^/IIII/' $fq #Add quality scores for added bases

            sed -i '4~4s/^/IIII/'  ${crIN}/$fq #Add quality scores for added bases

            echo "        converting UMI"

            sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/' $fq #Replace last 6 bases with AA

            sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/'  ${crIN}/$fq #Replace last 6 bases with AA

            echo "        converting quality scores"

            sed -i '4~4s/......$/II/' $fq #Replace quality scores for added bases

            sed -i '4~4s/......$/II/'  ${crIN}/$fq #Replace quality scores for added bases

        elif [[ "$technology" == "icell8" ]]; then

            echo "converting barcodes"

            sed -i '2~4s/^/AAAAA/' $fq #Add AAAAA to every read

            sed -i '2~4s/^/AAAAA/'  ${crIN}/$fq #Add AAAAA to every read

            echo "converting quality scores"

            sed -i '4~4s/^/IIIII/' $fq #Add quality scores for added bases

            sed -i '4~4s/^/IIIII/'  ${crIN}/$fq #Add quality scores for added bases

        fi

    done

    echo "    conversion complete"

        $d \

        $n \

        $j

#        --noexit

#        --nopreflight

end=`date +%s`