Fix output dir issue

src/workflow.py

@@ -6,6 +6,7 @@ from . import constant
 import os
 import re
 import json
+from pathlib import Path
 
 
 class Workflow:
@@ -14,7 +15,13 @@ class Workflow:
                  license = None, creativeWorkStatus = None, authors = None, 
                  version = None, keywords = None, producer = None,
                  publisher = None):
-        self.nextflow_file = Nextflow_File(file, duplicate = duplicate, display_info = display_info)
+        self.nextflow_file = Nextflow_File(
+            file,
+            duplicate=duplicate,
+            display_info=display_info,
+            output_dir=output_dir
+        )
+        self.output_dir = Path(output_dir)
         self.rocrate = None
         self.name = name
         self.datePublished = datePublished