Fixed some bugs

src/constant.py

@@ -123,7 +123,7 @@ END_PIPE_OPERATOR = r"\s*(\s*\|\s*\w+)+"
 
 #         PROCESS
 #--------------------------
-FILE = r'file +(\w+) *\n'
+FILE = r'file +(\w+) *\n|file +\( *(\w+) *\) *\n'
 FROM = r' from ([^\n]+)\n'
 INPUT = r"\n\s*input *:"
 INTO = r'into +([\w, ]+)'

src/process.py

@@ -354,7 +354,12 @@ class Process(Nextflow_Building_Blocks):
             #Case there is a single channel as an input -> doesn't use from to import channel -> uses file (see https://github.com/nextflow-io/nextflow/blob/45ceadbdba90b0b7a42a542a9fc241fb04e3719d/docs/process.rst)
             pattern = constant.FILE
             for match in re.finditer(pattern, line+"\n"):
-                extracted = match.group(1).strip()
+                #In the first case it's "file ch" in the second "file (ch)" 
+                try:
+                    extracted = match.group(1).strip()
+                except:
+                    extracted = match.group(2).strip()
+
                 add_channel(extracted)
                 self.raw_input_names.append(extracted)
             
@@ -581,6 +586,8 @@ class Process(Nextflow_Building_Blocks):
         for line in code.split("\n"):
             line = line.replace(" into ", ", emit: ")
             line = line.replace(" mode flatten", "")
+            #Remove optionnal true #TODO check if this breaks soemthing
+            line = line.replace("optional true", "")
             line = process_2_DSL2(line) 
             lines.append(line)
         code = "\n".join(lines)
@@ -590,8 +597,7 @@ class Process(Nextflow_Building_Blocks):
             def replacer(match):
                 return match.group(1)
             for o in line[1:]:
-                code = re.sub(fr"\,\s*{re.escape(o.get_code())}(\s|\,|\))", replacer, code)
-
+                code = re.sub(fr"\,\s*{re.escape(o.get_code())}(\s|\,|\))", replacer, code+"\n")
         return code
     
     #This method is to detect which are the channels which need to be flattened
@@ -609,13 +615,16 @@ class Process(Nextflow_Building_Blocks):
             if(bool(re.fullmatch(r"\w+\.val", raw_input_names[i]))):
                 raw_input_names[i] = raw_input_names[i].split('.')[0]
         return raw_input_names
-
+    
+    def get_parameters_call(self):
+        return ', '.join(self.clean_raw_input_names(self.raw_input_names))
+    
     def convert_to_DSL2(self):
         if(self.get_DSL()=="DSL2"):
             print("Workflow is already written in DSL2")
         else:
             code = self.get_code()
-            call = [f"{self.get_name()}({', '.join(self.clean_raw_input_names(self.raw_input_names))})"]
+            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())
             channels_to_flatten = self.get_channels_to_flatten()