Update the conversion from DSL1 to DSL2 -> there was a problem with the inputs and outputs

src/process.py

@@ -438,7 +438,11 @@ class Process(Nextflow_Building_Blocks):
             self.initialise_inputs_outputs()
 
     def convert_input_code_to_DSL2(self):
-        code = self.input_code
+        code = "\n"+self.get_input_code()+"\n"
+        code = remove_jumps_inbetween_parentheses(code)
+        code = remove_jumps_inbetween_curlies(code)
+        #Simplying the inputs -> when there is a jump line '.' -> it turns it to '.'
+        code = re.sub(constant.JUMP_DOT, '.', code)
         #code = process_2_DSL2(code) 
         lines = []
         for line in code.split("\n"):
@@ -448,7 +452,9 @@ class Process(Nextflow_Building_Blocks):
         return code
     
     def convert_output_code_to_DSL2(self):
-        code = self.output_code
+        code = self.get_output_code()
+        code = remove_jumps_inbetween_parentheses(code)
+        code = remove_jumps_inbetween_curlies(code)
         lines = []
         for line in code.split("\n"):
             line = line.replace(" into ", ", emit: ")