fixing path issues in nextflow translator

Author: rafaelfsilva

wfcommons/wfbench/translator/nextflow.py

@@ -194,16 +194,16 @@ def _create_task_script(output_folder: pathlib.Path, task: Task):
         # Generate input spec
         input_spec = "'\\["
         for f in task.input_files:
-            input_spec += f"\"data/{f.file_id}\","
+            input_spec += f"\"{output_folder.resolve()}/data/{f.file_id}\","
         input_spec = input_spec[:-1] + "\\]'"
 
         # Generate output spec
         output_spec = "'\\{"
         for f in task.output_files:
-            output_spec += f"\"data/{f.file_id}\":{str(f.size)},"
+            output_spec += f"\"{output_folder.resolve()}/data/{f.file_id}\":{str(f.size)},"
         output_spec = output_spec[:-1] + "\\}'"
 
-        code += f"bin/{task.program} "
+        code += f"{output_folder.resolve()}/bin/{task.program} "
 
         for a in task.args:
             if "--output-files" in a: