Moved the conditions to the outside of the cluster in the case of one...

Moved the conditions to the outside of the cluster in the case of one condition in cluster + added the creation of empty channels

src/workflow.py

@@ -3,7 +3,7 @@
 from .nextflow_file import Nextflow_File
 from .ro_crate import RO_Crate
 from . import constant
-from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs
+from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs, extract_curly
 from .outils_graph import flatten_dico, initia_link_dico_rec, get_number_cycles
 from .outils_annotate import get_tools_commands_from_user_for_process
 from .bioflowinsighterror import BioFlowInsightError
@@ -933,6 +933,18 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                             #TODO find a better naming system
                             name = f"non_relevant_cluster_{non_relevant_name}"
                             non_relevant_name+=1
+
+                    #Check that there is a single condtion in the body
+                    body = group_together_ifs(body)
+                    conditions_in_subworkflow = []
+                    end = -1
+                    for match in re.finditer(r"if\s*(\([^\{]+)\{", body):
+                        conditions_in_subworkflow.append(match.group(1).strip())
+                        _, start = match.span(0)
+                        
+                    if(len(conditions_in_subworkflow)==1):
+                        end = extract_curly(body, start)
+                        body = body[start: end-1].strip()
                     
 
                     #TAKE
@@ -965,38 +977,40 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
                     #Replace names inside subworkflow
                     subworkflow_code = f"subworkflow {name} {{\n{take}\n{body}\n{emit}\n}}"
-                    params = ", ".join(old_param_names)
-                    subworkfow_call = f"{name}({params})"
-                    
                     for i in range(len(new_param_names)):
                         pattern = fr"[\=\,\(] *({re.escape(takes_param[i].get_code())})[\s\,\)]"
                         subworkflow_code = replace_group1(subworkflow_code, pattern, new_param_names[i])
                         #subworkflow_code = subworkflow_code.replace(takes_param[i].get_code(), new_param_names[i])
                     
+                    #TODO -> added verification of conditions 
+                    params = ", ".join(old_param_names)
+                    subworkfow_call_case_true = f"{name}({params})"
+                    subworkfow_call_case_false = ""
                     for i in range(len(new_output_names)):
                         #In the case of channels, we just add chanel = subworkflow.out[i]
                         if(not bool(re.findall("\.\s*out", old_output_names[i]))):
-                            subworkfow_call+=f"\n{old_output_names[i]} = {new_output_names[i]}"
+                            subworkfow_call_case_true+=f"\n{old_output_names[i]} = {new_output_names[i]}"
+                            subworkfow_call_case_false+=f"\n{old_output_names[i]} = Channel.empty()"
                         #In the case of emitted values we need to replace the code on the outside
                         else:
                             param_out_name= f"{name}_out_{i+1}"
-                            subworkfow_call+=f"\n{param_out_name} = {new_output_names[i]}"
+                            subworkfow_call_case_true+=f"\n{param_out_name} = {new_output_names[i]}"
+                            subworkfow_call_case_false+=f"\n{param_out_name} = Channel.empty()"
                             channels_to_replace_outside_of_cluster.append((old_output_names[i], param_out_name))
+                    #If there was only one single condition in the subworkflow cluster -> then we add it when the call is done
+                    if(len(conditions_in_subworkflow)==1):
+                        subworkfow_call = f"if{conditions_in_subworkflow[0]} {{\n{subworkfow_call_case_true}\n}} else {{\n{subworkfow_call_case_false}\n}}"
+                        None
+                    else:
+                        subworkfow_call = subworkfow_call_case_true
 
 
                     subworkflow_clusters_to_add.append(subworkflow_code)
                     subworkflow_cluster_calls_to_add.append(subworkfow_call)
                     index_cluster+=1
-                    subworkflow_code = format_with_tabs(group_together_ifs(subworkflow_code))
-                    #subworkflow_code = format_with_tabs(subworkflow_code)
-                    print(subworkflow_code)
-                    #print(subworkfow_call)
-                    #
-                    #for t in self.get_takes(things_added_in_cluster):
-                    #    print("*", t.get_code())
-                    #
-                    #for t in self.get_emits(things_added_in_cluster):
-                    #    print("-", t.get_code())
+                    
+                
+                    print(format_with_tabs(subworkflow_code))
                     print("-----------")