Updated the DSL1 conversion

src/nextflow_file.py

@@ -333,9 +333,16 @@ class Nextflow_File(Nextflow_Building_Blocks):
                 
                 #Replacing the processes and functions defined with their identifiers -> this is to simplifly the analysis with the conditions
                 for process in self.processes:
-                    code = code.replace(process.get_code(), f"process: {str(process)}")
+                    temp = code
+                    code = code.replace(process.get_code(get_OG = True), f"process: {str(process)}")
+                    if(temp==code):
+                        print(process.get_code())
+                        raise Exception("Something went wrong the code hasn't changed")
                 for function in self.functions:
-                    code = code.replace(function.get_code(), f"function: {str(function)}")
+                    temp = code
+                    code = code.replace(function.get_code(get_OG = True), f"function: {str(function)}")
+                    if(temp==code):
+                        raise Exception("Something went wrong the code hasn't changed")
                 self.main = Main(code= code, nextflow_file=self)
                 self.main.initialise()
                 

src/process.py

@@ -499,8 +499,10 @@ class Process(Nextflow_Building_Blocks):
         else:
             code = self.get_code()
             call = [f"{self.get_name()}({self.get_parameters_call()})"]
-            code = code.replace(self.input_code, self.convert_input_code_to_DSL2())
-            code = code.replace(self.output_code, self.convert_output_code_to_DSL2())
+            if(self.input_code!=""):
+                code = code.replace(self.input_code, self.convert_input_code_to_DSL2())
+            if(self.output_code!=""):
+                code = code.replace(self.output_code, self.convert_output_code_to_DSL2())
             channels_to_flatten = self.get_channels_to_flatten()
  
 

src/workflow.py

@@ -347,7 +347,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             for p in nextflow_file.get_processes():
                 new_process, call = p.convert_to_DSL2()
                 processes.append(new_process)
-                to_replace.append((p.get_code(), call))
+                to_replace.append((p.get_code(get_OG = True), call))
             
             for r in to_replace:
                 code = code.replace(r[0], r[1])
@@ -363,7 +363,14 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
             #Putting || back
             code = code.replace("$OR$", "||")
-            self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=False)
+           
+            #Somethimes this is incorrect but that's due to the fact that the DSL1 analysis isn't as clean as the DSL2 analyse (concerning the conditions)
+            #What i mean that when searching for channels, DSL1 doesn't consider the conditions when searching from the processes while DSL2 does
+            #The conversion works well but it's just comparing to the old DSL1 workflow doesn't make sense
+            #If you want to put this line back you need #TODO update the DSL1 parsing to consider the blocks when defining the processes 
+            #A good example is KevinMenden/hybrid-assembly
+            #self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=True)
+            
             return code
     
     #This methods generates a random set of processes to consider as relavant 
@@ -474,7 +481,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 raise Exception("This shoudn't happen")
 
         #Simplifying main
-        code = code.replace(self.get_workflow_main().get_code(), self.get_workflow_main().simplify_code())
+        code = code.replace(self.get_workflow_main().get_code(get_OG = True), self.get_workflow_main().simplify_code())
 
 
         #Adding processes into code
@@ -576,7 +583,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
     def rewrite_subworkflow_call(self, code, subworklfow):
         
         #Remove the defintion from the code
-        code = code.replace(subworklfow.get_code(), "")
+        code = code.replace(subworklfow.get_code(get_OG = True), "")
         OG_call = subworklfow.get_call()
         OG_body = subworklfow.get_work()