From f67d9fe641183b173acb109426b02ee67c9fea3d Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Mon, 20 May 2019 11:48:16 -0500
Subject: [PATCH] Check Directory Path in mkfastq
---
workflow/main.nf | 35 ++++++++++++++++-------------------
1 file changed, 16 insertions(+), 19 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 8792630..45175a6 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -37,14 +37,7 @@ process checkDesignFile {
"""
hostname
ulimit -a
- dL=`echo "$designLocation" | tr -d ' '`
- if [ `dirname "$designLocation"` != `dirname "\$dL"` ]
- then echo "Error: Spaces Found in Design Directory Path"
- exit 5
- elif [ `basename "$designLocation"` != `basename "\$dL"` ]
- then mv "$designLocation" "\$dL"
- fi
- python3 "$baseDir/scripts/check_design.py" -d "\$dL"
+ python3 "$baseDir/scripts/check_design.py" -d "$designLocation"
"""
}
@@ -67,19 +60,10 @@ process untarBCL {
"""
hostname
ulimit -a
-
- tar_no=`echo "${tar}" | tr -d ' '`
- if [ `dirname "${tar}"` != `dirname "\${tar_no}"` ]
- then echo "Error: Spaces Found in BCL Directory Path"
- exit 5
- elif [ `basename "${tar}"` != `basename "\$dL"` ]
- then mv "${tar}" "\${tar_no}"
- fi
-
name=`echo ${tar} | rev | cut -f1 -d '.' | rev`;
if [ "\${name}" == "gz" ];
- then tar -xvf "\$tar_no" -I pigz;
- else tar -xvf "\$tar_no";
+ then tar -xvf "$tar" -I pigz;
+ else tar -xvf "$tar";
fi;
"""
}
@@ -107,6 +91,19 @@ process mkfastq {
"""
hostname
ulimit -a
+
+ bcl_no=`readlink -e "${bcl}" | tr -d ' '`
+ if [ `dirname "${bcl}"` != `dirname "\${bcl_no}"` ]
+ then echo "Error: Spaces Found in BCL Directory Path"
+ exit 5
+ fi
+
+ dL=`readlink -e "$design" | tr -d ' '`
+ if [ `dirname "$design"` != `dirname "\$dL"` ]
+ then echo "Error: Spaces Found in Design Directory Path"
+ exit 5
+ fi
+
cellranger mkfastq --id="${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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