Commit 5e3a85b8 authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Directory Check

parent f67d9fe6
Pipeline #3919 passed with stages
in 2 minutes
......@@ -91,17 +91,20 @@ process mkfastq {
"""
hostname
ulimit -a
bcl_no=`readlink -e "${bcl}" | tr -d ' '`
bcl_no=`readlink -e "$bcl" | tr -d ' '`
if [ `dirname "${bcl}"` != `dirname "\${bcl_no}"` ]
then echo "Error: Spaces Found in BCL Directory Path"
exit 5
exit 13
fi
dL0=`readlink -e "$design"`
dL=`readlink -e "$design" | tr -d ' '`
if [ `dirname "$design"` != `dirname "\$dL"` ]
echo "\$dL"
echo "\$dL0"
if [ `dirname "\$dL0"` != `dirname "\$dL"` ]
then echo "Error: Spaces Found in Design Directory Path"
exit 5
exit 13
fi
cellranger mkfastq --id="${bcl.baseName}" --run="$bcl" --csv=$design -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
......
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