minor bug fixes and error message for having a period in the sample name.

install=false

######convert version#####

convertversion="0.3.0.9002"

convertversion="0.3.0.900333"

##########

####cellrenger version#####

cellrangerpath=`which cellranger` #location of cellranger

if [[ -z $cellrangerpath ]]; then

    echo "checking options ..."

fi

#check if this is a test run

if [[ $testrun == "true" ]]; then

    reference=${SDIR}/test/cellranger_reference/cellranger-tiny-ref/3.0.0

    if [[ -z $id ]]; then

        id=test-tiny-${technology}

    fi

    if [[ $technology == "10x" ]]; then

        gunzip -k ${SDIR}test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

        read1=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")

        read2=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

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

        gunzip -k test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq

        read1=("test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")

        read2=("test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")

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

        gunzip -k test/shared/mappa-test/test_FL_R[12].fastq.gz

        read1=("test/shared/mappa-test/test_FL_R1.fastq")

        read2=("test/shared/mappa-test/test_FL_R2.fastq")

    fi

fi

#check if cellranger is writable

if ! [[ -w "$barcodedir" ]]; then

    echo "Kai $barcodedir"

    echo "Error: Trying to run cellranger installed at ${cellrangerpath}"

    echo "launch_universc.sh can only run with cellranger installed locally"

    echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"

    fi

fi

if [[ $testrun == "true" ]]; then

     reference=${SDRI}/test/cellranger_reference/cellranger-tiny-ref/3.0.0"

     if [[ -z $id ]] then

         id=test-tiny-${technology}

     fi

     if [[ $technology == "10x" ]]; then

         gunzip -k ${SDIR}test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

         read1=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")

         read2=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

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

         gunzip -k test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq

         read1=("test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")

         read2=("test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")

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

          gunzip -k test/shared/mappa-test/test_FL_R[12].fastq.gz

          read1=("test/shared/mappa-test/test_FL_R1.fastq)

          read2=("test/shared/mappa-test/test_FL_R2.fastq")

    fi

fi

#check for presence of read1 and read2 files

if [[ $setup == "false" ]]; then

    if [[ ${#read1[@]} -eq 0 ]]; then

#checking the quality of fastq file names

read12=("${read1[@]}" "${read2[@]}")

for fq in "${read12[@]}"; do

    name=`basename $fq | cut -f1 -d'.' | grep -o "_" | wc -l | xargs`

    sn=`basename $fq | cut -f1-$(($name-3))  -d'_'`

    ln=`basename $fq | cut -f$(($name-1))  -d'_' | sed 's/L00//'`

    name=`basename $fq`

    name=${name%.*}

    sn=`echo ${name} | cut -f1 -d'_'`

    ln=`echo ${name} | cut -f3 -d'_' | sed 's/L00//'`

    fields=`echo ${name} | grep -o "_" | wc -l`

    fields=$(($fields+1))

    LANE+=($ln)

    if [[ $name < 4 ]]; then

    if [[ ${fields} != 5 ]]; then

        echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";

        exit 1

    elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then

        echo "Error: $fq does not have a .fq or .fastq extention."

        exit 1

    elif [[ ${sn} =~ "." ]]; then

        echo "Error: $fq has a period \".\" within its sample name. Remove it to run cellranger."

	exit 1

    fi

    if [[ $sn != $SAMPLE ]]; then

    if [[ ${sn} != $SAMPLE ]]; then

        if [[ -z $SAMPLE ]]; then

            SAMPLE=$sn

            SAMPLE=${sn}

        else

            echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."

            exit 1

#####convert file format#####

echo "converting input files to confer cellranger format ..."

if [[ $convert == "false" ]]; then

    echo " input file format conversion skipped"

fi

echo "barcodes:" $barcodeadjust "umis:" $umiadjust 

echo " barcodes: ${barcodeadjust}bps at its head"

echo " UMIs: ${umiadjust}bps at its tail" 

#converting barcodes

echo " adjusting barcodes of R1 files"