Just updated one or two small things

src/call.py

@@ -201,6 +201,9 @@ class Call(Executor):
                     raise Exception("This shouldn't happen")
         return code.split()
 
+    def get_artificial_status(self):
+        return False
+
     def analye_parameters(self, param):
 
         #Step 1 -> get parameters

src/main.py

@@ -19,13 +19,13 @@ class Main(Nextflow_Building_Blocks):
         executors = self.get_all_executors_in_subworkflow()
         pos = {}
         for e in executors:
-            code = e.get_code(get_OG = True)
-            #We don't have to check the calls -> since there are renamed with their ids when we rewrite the code -> so it solve the issue
-            if(code in seen and e.get_type()=="Operation"):
-                raise BioFlowInsightError(f'Operation "{code}" appears twice in the workflow in the exact same way. BioFlow-Insight cannot rewrite the workflow then, try slighly changing how one of the executors is defined', type = "Rewrite Error")
-            seen[code] = ''
-            pos[e] = e.get_position_in_main(e)
-        #TODO add sort here
+            if(not e.get_artificial_status()):
+                code = e.get_code(get_OG = True)
+                #We don't have to check the calls -> since there are renamed with their ids when we rewrite the code -> so it solve the issue
+                if(code in seen and e.get_type()=="Operation"):
+                    raise BioFlowInsightError(f'Operation "{code}" appears twice in the workflow in the exact same way. BioFlow-Insight cannot rewrite the workflow then, try slighly changing how one of the executors is defined', type = "Rewrite Error")
+                seen[code] = e
+                pos[e] = e.get_position_in_main(e)
         pos =  {k: v for k, v in sorted(pos.items(), key=lambda item: item[1])}
         for e in pos:
             if(e.get_type()=="Call"):

src/outils.py

@@ -1620,7 +1620,12 @@ def extract_tools(script, extract_general_tools = False):
                                     tools.append("perl")
                                 elif(extension==".jl"):
                                     tools.append("julia")
-                        elif (ex!="" and len(ex)>1 and ex not in general_tools and ex[-1]!=":" and re.fullmatch(r"\w", ex[0])):
+                        elif (ex!="" 
+                              and len(ex)>1 
+                              and ex not in general_tools 
+                              and ex[-1]!=":" 
+                              and re.fullmatch(r"\w", ex[0])
+                              and "=" not in ex):
                             tools.append(ex)
                         #If the tool is java -> we search for the jar file in the command
                         if(ex=="java"):

src/workflow.py

@@ -436,9 +436,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 for p in sampled:
                     name_select.append(p.get_alias())
                 return name_select
-            else:
-                print("here")
-        
+
 
     #This methods generates a random set of processes to consider as relavant 
     def generate_random_relevant_processes(self, alpha = -1):