-p option (former --overwrite option) cleaned up and implemented.

  -c,  --chemistry CHEM         Assay configuration, autodetection is not possible for converted files: 'SC3Pv2' (default), 'SC5P-PE', or 'SC5P-R2'

  -n,  --force-cells NUM        Force pipeline to use this number of cells, bypassing the cell detection algorithm.

  -j,  --jobmode MODE           Job manager to use. Valid options: 'local' (default), 'sge', 'lsf', or a .template file

  -w,  --overwrite              How to carry out FASTQ file conversions: 'skip' to skip conversion, 'convert' to overwrite all preexisting converted files, and 'keep' (default) to only convert files that do not already exist.

  -p,  --pass                   Skips the FASTQ file conversion if converted files already exist

  -h,  --help                   Display this help and exit

  -v,  --version                Output version information and exit

       --verbose                Print additional outputs for debugging

#variable options

setup=false

convert=true

read1=()

read2=()

SAMPLE=""

ncells=""

chemistry=""

jobmode=""

convert=keep

next=false

for op in "$@"; do

                exit 1

            fi

            ;;

        -w|--overwrite)

            shift

            if [[ "$1" != "" ]]; then

                convert="${1/%\//}"

                next=true

        -p|--pass)

            convert=false

            next=false

            shift

            else

                echo "Error: value missing for --overwrite"

                exit 1

            fi

            ;;

        --verbose)

            echo "debugging mode activated"

#check for file type (extension) for files

##allows incomplete file names and processing compressed files

#test

#read12=( $read1, $read2 )

#for i in ${read12[@]}; do

#    echo "KAI! $i"

#done

for i in ${!read1[@]}; do

    read=${read1[$i]}

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

done

LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//')

#check if ID is present

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

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

        echo "Error: option --id is required"

        exit 1

    fi

elif [[ $id == *" "* ]]; then

    echo "Error: \"$id\" for option -id must not contain a space"

    exit 1

fi

#check if reference is present

if [[ -z $reference ]]; then

    if [[ $setup == "false" ]] || [[ ${#read1[@]} -ne 0 ]] || [[ ${#read2[@]} -ne 0 ]]; then

    exit 1

fi

#check if conversion matches expected input

if [[ "$convert" != "keep" ]] && [[ "$convert" != "skip" ]] && [[ "$convert" != "convert" ]]; then

    echo "Error: option --overwrite needs to be keep, skip, or convert"

    exit 1

fi

#check if setup needs to be run before analysis

if [[ -z $setup ]]; then

    setup=false

if [[ $lastcall != $technology ]]; then

    setup=true

fi

#check if ID is present

if [[ -z $id ]]; then

    if [[ ${#read1[@]} -ne 0 ]] || [[ ${#read2[@]} -ne 0 ]]; then

        echo "Error: option --id is required"

        exit 1

    fi

fi

##########

echo "creating a folder for all cellranger input files ..."

convFiles=()

if [[ ! -d $crIN ]]; then

if [[ ! -d $crIN ]] || [[ $lastcall != $technology ]]; then

    echo " directory $crIN created for converted files"

    convert=true

    if [[ -d $crIN ]]; then

        rm -rf $crIN

    fi

    mkdir $crIN

else

    echo " directory $crIN already exists"

fi

echo "moving files to new location"

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

    echo "moving file to new location"

fi

crR1s=()

for fq in "${read1[@]}"; do

    to=`basename $fq`

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

    crR1s+=($to)

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

        echo "handling $fq ..."

        convFiles+=($to)

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

            gunzip -c $fq > $to

        else

            cp -T $fq $to

        fi

    elif [[ $convert == "keep" ]] && [[ ! -f $to ]]; then

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

        echo " handling $fq ..."

        convFiles+=($to)

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

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

    crR2s+=($to)

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

        echo " handling $fq ..."

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

            gunzip -c $fq > $to

        else

            cp -T $fq $to

        fi

    elif [[ $convert == "keep" ]] && [[ ! -f $to ]]; then

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

        echo " handling $fq ..."

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

            gunzip -c $fq > $to

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

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

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

    echo " input file format conversion skipped"

fi

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

    echo " 10x files accepted without conversion"

else

elif [[ $convert == "true" ]]; then

    echo " converting file from $technology format to 10x format ..."

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

        echo " handling $convFile ..."