first stab at getting new runner script working

scripts/run_Processor.sh

 #!/bin/bash
 
+original_args=("$@")
+
 SHORT=p:h
 OPTS=$(getopt -a --options $SHORT -- "$@")
 echo $OPTS
@@ -72,7 +74,7 @@ proc_path="$( dirname "$(readlink -f "$0" )" )"
 # run the processor with all arguments
 processor=${proc_path}/../coordinator/${processor_class}
 printf "processor is %s\n\n" "$processor"
-python  "${processor}" "$@"
+python  "${processor}" "${original_args[@]}"
 exit_code=$?;
 
 # deactivate conda environment