Remove output directory from shell execution to avoid directory to be removed...

Remove output directory from shell execution to avoid directory to be removed when a rerun is called.

workflows/components/normalizerawcount.py

@@ -82,7 +82,7 @@ class NormalizeRawCount (ComponentAnalysis):
         
     
     def process(self):
-        self.add_shell_execution(self.get_exec_path("Rscript")+ " "+ self.get_exec_path("Normalization.R") + " -f $1 -o $2 > $3 2>> $4",
+        self.add_shell_execution(self.get_exec_path("Rscript")+ " "+ self.get_exec_path("Normalization.R") + " -f $1 -o `dirname $2` > $2 2>> $3",
                                  cmd_format='{EXE} {IN} {OUT} ',
-                                 inputs=self.matrix, outputs=[self.output_directory,self.stdout,self.stderr]+self.files)
+                                 inputs=self.matrix, outputs=[self.stdout,self.stderr]+self.files)
       
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