Commit 04e8fe78 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct passing optional args to cellranger

parent ae56aea4
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+11 −3
Original line number Diff line number Diff line
@@ -494,6 +494,14 @@ if [[ -z $keep ]]; then
    keep=false
fi

if [ -z "$ncells" ]; then
    ncells=null
else
    if ! [[ $ncells =~ '^[0-9]+$' ]] ; then
        error "--force-cells must be a number"
    fi
fi


#report inputs
echo technology: $technology
@@ -879,15 +887,15 @@ fi
#running cellranger
echo "    running cellranger..."
d=""
if [[ ! $description ]]; then
if [[ -n $description ]]; then
    d="--description=$description"
fi
n=""
if [[ ! $ncells ]]; then
if [[ -n $ncells ]]; then
    n="--force-cells=$ncells"
fi
j=""
if [[ ! $jobmode ]]; then
if [[ -n $jobmode ]]; then
    j="--jobmode=$jobmode"
fi
start=`date +%s`