avoid deleting concurrent runs (check converted files exist)

#create directory of modified files

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

crIN="cellranger"

rm -rf $crIN

mkdir $crIN

mkdir -p $crIN

if [ -d $crIN ]

    then

    for i in ${!read1[@]}

    do

        read=${read1[$i]}

        if [ -f $crIN/$read ] 

            then

            echo "warning: converted $read file already exists"

        fi

        rm -rf $crIN/$read

    done

    for i in ${!read2[@]}

    do

        read=${read2[$i]}

        if [ -f $crIN/$read ]

            then

            echo "warning: converted $read file already exists"

        fi

        rm -rf $crIN/$read

    done

fi

crR1s=()

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