Move untarBCl to Script

workflow/main.nf

@@ -60,20 +60,7 @@ process untarBCL {
   """
   hostname
   ulimit -a
- 
-  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";
-  fi;
+  bash "$baseDir/scripts/untarBCL.sh" -t "$tar"
   """
 }
 

workflow/scripts/untarBCL.sh

+#!/bin/bash
+#untarBCL.sh
+
+usage() {
+  echo "-t  --tar file"
+  exit 1
+}
+OPTIND=1
+while getopts :t: opt
+do
+   case $opt in
+	t) tar=$OPTARG;;
+   esac
+done
+
+shift $(($OPTIND -1));
+
+echo "This Line"
+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";
+fi;