Change path to scripts R

src/ng6/utils.py

@@ -300,7 +300,7 @@ class Utils(object):
         """
         group_basenames = {}
 
-        for file in file_list:      
+        for file in file_list:  
             file_name_fields = os.path.basename(file).split(Utils.CASAVA_FILENAME_SEPARATOR)
         
             group_tag = Utils.CASAVA_FILENAME_SEPARATOR.join( file_name_fields[:Utils.CASAVA_FILENAME[group_by]] )
@@ -309,7 +309,7 @@ class Utils(object):
                 group_basenames[group_tag].append(file)
             else:
                 group_basenames[group_tag] = [file]
-     
+        logging.getLogger("Utils").debug("get_group_basenames. group_basenames = " + ",".join(group_basenames))
         return group_basenames
 
     @staticmethod

workflows/ont_qc/components/run_stats.py

@@ -227,14 +227,14 @@ class Run_stats (Analysis):
         #print (self.sequencing_summary_file)
         
         
-        self.add_shell_execution(self.get_exec_path("Rscript") +" /work/ng6-test/claire/test_ont_qc/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2', 
+        self.add_shell_execution(self.get_exec_path("Rscript") +" /save/sbsuser/scripts-ngs/current/ont/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2', 
                                 cmd_format='{EXE} {IN} {OUT}' ,
                                 map=False, 
                                 inputs = self.sequencing_summary_file,
                                 outputs = self.stderr)
         
         if self.barcoded == "yes" :
-            self.add_shell_execution(self.get_exec_path("Rscript") +" /work/ng6-test/claire/test_ont_qc/graph_albacoresummary_barcode.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2', 
+            self.add_shell_execution(self.get_exec_path("Rscript") +" /save/sbsuser/scripts-ngs/current/ont/graph_albacoresummary_barcode.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2', 
                                 cmd_format='{EXE} {IN} {OUT}' ,
                                 map=False, 
                                 inputs = self.sequencing_summary_file,