Commit e94c5b4a authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Check unTar String Directory for spaces

parent 5e3a85b8
Pipeline #3935 passed with stages
in 1 minute and 48 seconds
......@@ -60,7 +60,16 @@ process untarBCL {
"""
hostname
ulimit -a
name=`echo ${tar} | rev | cut -f1 -d '.' | rev`;
folder=\$(tar -tf "$tar" | grep -o "^[^/]*/\$")
folder1=`echo "\$folder" | tr -d ' '`
if [ "\$folder" != "\$folder1" ]
then echo "Error: Spaces found in BCL Directory Path"
echo "\$folder"
exit 21
fi
name=`echo "${tar}" | rev | cut -f1 -d '.' | rev`;
if [ "\${name}" == "gz" ];
then tar -xvf "$tar" -I pigz;
else tar -xvf "$tar";
......@@ -68,7 +77,6 @@ process untarBCL {
"""
}
process mkfastq {
tag "${bcl.baseName}"
queue '128GB,256GB,256GBv1,384GB'
......@@ -90,23 +98,7 @@ process mkfastq {
"""
hostname
ulimit -a
bcl_no=`readlink -e "$bcl" | tr -d ' '`
if [ `dirname "${bcl}"` != `dirname "\${bcl_no}"` ]
then echo "Error: Spaces Found in BCL Directory Path"
exit 13
fi
dL0=`readlink -e "$design"`
dL=`readlink -e "$design" | tr -d ' '`
echo "\$dL"
echo "\$dL0"
if [ `dirname "\$dL0"` != `dirname "\$dL"` ]
then echo "Error: Spaces Found in Design Directory Path"
exit 13
fi
ulimit -a
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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