Added functions to DSL2

src/workflow.py

@@ -626,10 +626,11 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
             include_section = f"//INCLUDE_SECTION_{tag}"
             params_section = f"//PARAMS_SECTION_{tag}"
+            function_section = f"//FUNCTION_SECTION_{tag}"
             process_section = f"//PROCESS_SECTION_{tag}"
 
 
-            code = code.replace(code_to_replace, f"""{start_code}\n\n{include_section}\n\n{params_section}\n\n{process_section}\n\nworkflow{{\n\n{body}\n}}\n\n""")
+            code = code.replace(code_to_replace, f"""{start_code}\n\n\n{include_section}\n\n\n{params_section}\n\n\n{function_section}\n\n\n{process_section}\n\n\nworkflow{{\n\n{body}\n}}\n\n""")
 
             params_list = []
             for match in re.finditer(r"params.\w+ *\= *[^\n=]([^\n])*", code):
@@ -638,8 +639,21 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 code = code.replace(params, "")
             params_code = "\n".join(params_list)
             code = code.replace(params_section, params_code)
+
+
+            #Moving Functions
+            functions = []
+            for f in self.nextflow_file.functions:
+                function = f.get_code()
+                functions.append(function)
+
+            for r in functions:
+                code = code.replace(r, "")
+            code = code.replace(function_section, "\n\n".join(functions))
+    
             
 
+            #Moving Processes
             processes = []
             to_replace = []
             for p in self.nextflow_file.get_processes():
@@ -659,6 +673,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 else:
                     raise Exception(f"Executor of type '{o.get_type()}' was extracted in a DSL1 workflow! This shoudn't happen! The code is '{o.get_code()}'")
             #print(code)
+   
             return code
             #print(code)
             #