Fix weird bug which wasn't connecting processes in rewritting

src/workflow.py

@@ -734,10 +734,16 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             subworkflow_clusters_to_add, subworkflow_cluster_calls_to_add = [], []
             index_cluster = 0
             for elements in clusters:
+                #Check that there is at least one process in cluster
+                at_least_one_process = False
+                for e in elements:
+                    if(e.get_type()=="Process"):
+                        at_least_one_process = True
+
                 #Only create the subworkflows for clusters with more than one element
                 processes_added = []
                 things_added_in_cluster = []
-                if(len(elements)>1):
+                if(len(elements)>1 and at_least_one_process):
                     name, body, take, emit = "", "", "", ""
                     first_element = True
                     for ele in elements:
@@ -781,6 +787,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                                     code = code.replace(ele.get_code(get_OG = True), "", 1)
                 
                                 #Ignore these cases
+                                #TODO -> you should be able to remove this
                                 if(ele.get_code()[:4] not in ["emit", "take"]):
                                     origins = ele.get_origins()
                                     for o in origins:
@@ -839,8 +846,14 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                     new_param_names, index, old_param_names = [], 1, []
                     for param in takes_param:
                         param_name = f"param_{name}_{index}"
-                        new_param_names.append(param_name)
-                        old_param_names.append(param.get_code())
+                        #Here if the input is a channel -> we keep the same name for readibility
+                        #It also solves a bug described on the 18/02/2025
+                        if(param.get_type()!='Channel'):
+                            new_param_names.append(param_name)
+                            old_param_names.append(param.get_code())
+                        else:
+                            new_param_names.append(param.get_code())
+                            old_param_names.append(param.get_code())
                         index += 1
                     if(len(new_param_names)>0):
                         temp = '\n'.join(new_param_names)