Merge pull request #80 from wfcommons/nextflow_improvements

Nextflow improvements

Author: rafaelfsilva

wfcommons/wfbench/translator/nextflow.py

@@ -227,8 +227,8 @@ def _generate_task_code(self, task: Task) -> str:
         :return: The code.
         :rtype: str
         """
-
-        code = f"process {task.task_id}()" + "{\n"
+        function_name = task.task_id.replace(".", "_")
+        code = f"process {function_name}()" + "{\n"
 
         # File variables
         if self._find_children(task.task_id):
@@ -318,22 +318,22 @@ def _generate_task_function(self, task: Task) -> str:
 
         if self._find_parents(task.task_id):
             # Input channel mixing and then call
-            code += f"\tdef {task.task_id}_necessary_input = Channel.empty()\n"
+            code += f"\tdef {function_name}_necessary_input = Channel.empty()\n"
             for f in task.input_files:
-                code += f"\t{task.task_id}_necessary_input = {task.task_id}_necessary_input.mix(inputs.{f.file_id})\n"
-            code += f"\tdef {task.task_id}_necessary_input_future = {task.task_id}_necessary_input.collect()\n"
-            code += f"\tdef {task.task_id}_produced_output = {task.task_id}({task.task_id}_necessary_input_future)\n"
+                code += f"\t{function_name}_necessary_input = {function_name}_necessary_input.mix(inputs.{f.file_id})\n"
+            code += f"\tdef {function_name}_necessary_input_future = {function_name}_necessary_input.collect()\n"
+            code += f"\tdef {function_name}_produced_output = {function_name}({function_name}_necessary_input_future)\n"
         else:
             # Simple call
-            code += f"\tdef {task.task_id}_produced_output = {task.task_id}()\n"
+            code += f"\tdef {function_name}_produced_output = {function_name}()\n"
 
         # Pass on the outputs
         code += "\n"
         code += "\tdef outputs = inputs.clone()\n"
         if self._find_children(task.task_id):
             counter = 0
             for f in task.output_files:
-                code += f"\toutputs.{f.file_id} = {task.task_id}_produced_output.map" + "{it[" + str(counter) + "]}\n"
+                code += f"\toutputs.{f.file_id} = {function_name}_produced_output.map" + "{it[" + str(counter) + "]}\n"
                 counter += 1
         code += "\treturn outputs\n"
         code += "}\n\n"