conflicts magically removed

#####usage statement#####

#get shell

## detect shell across different OS

if [[ $VENDOR != "apple" ]]

    then

    SHELL=$(readlink -f /proc/$$/exe | cut -d'/' -f3)

else

    SHELL=$(ps -p $$ | awk '$1 == PP {print $4}' PP=$$)

fi

## detect how called (e.g., bash converrt.sh or ./launch_universc.sh)

if [[ $(which launch_universc.sh) != *"not found" ]]

    then

    SHELL='' 

    invocation=$0

if [[ -n $BASH_VERSION ]]; then

    invocation='bash '${invocation}''

elif [[ -n $ZSH_VERSION ]]; then

    invocation='zsh '${invocation}''

elif [[ -n $FISH_VERSION ]]; then

    invocation='fish '${invoaction}''

elif [[ -n $KSH_VERSION ]]; then

    invocation='ksh '${invocation}''

else

    if [[ -z $ZSH_VERSION ]]

        then

        SHELL="zsh"

    elif [[ -z $KSH_VERSION ]]

       then

       SHELL="ksh"

    elif [[ -z $FISH_VERSION ]]

       then

       SHELL="fish"

    elif [[ -z $BASH_VERSION ]]

        then

        SHELL="bash"

    else

       SHELL=$SHELL

    fi

    invocation=$(echo $(basename $0))

fi

#usage statement

help='

Usage:

  '$invocation' --testrun -t TECHNOLOGY

  '$invocation' -t TECHNOLOGY --setup

  '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$invocation' -v

  '$invocation' -h

  '$SHELL' '$invocation' --testrun -t TECHNOLOGY

  '$SHELL' '$invocation' -t TECHNOLOGY --setup

  '$SHELL' '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  '$SHELL' '$invocation' -v

  '$SHELL' '$invocation' -h

Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count

if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

    fi

    echo "  number of these files are as expected"

fi

if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

    fi

    echo "  files exist, with extentions compatible with launch_universc.sh"

fi

##########

#####Input file curation 3: renaming read1, read2, index1, and index2 file name if not compatible with the convet.sh#####

#####Input file curation 3: renaming read1, read2, index1, and index2 file name if not compatible with the launch_universc.sh#####

for key in ${keys[@]}; do

    readkey=$keys

    list=""

if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

    fi

    echo "  names of these files are compatible with launch_universc.sh"

fi

##########

if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

    fi

    echo "  input files adjusted for technology-specific conditions"

fi

##########

echo "#####cellranger command#####"

start=`date +%s`

echo "cellranger count --id=$id

        --fastqs=$crIN

        --lanes=$LANE

        --r1-length=$totallength

        --chemistry=$chemistry

        --transcriptome=$reference

        --sample=$SAMPLE

        $d

        $n

        $j

        $l

echo "cellranger count --id=$id\\

        --fastqs=$crIN\\

        --lanes=$LANE\\

        --r1-length=$totallength\\

        --chemistry=$chemistry\\

        --transcriptome=$reference\\

        --sample=$SAMPLE\\

        $d\\

        $n\\

        $j\\

        $l\\

        $m

"

echo "##########"