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Author: jan-janssen

python_workflow_definition/src/python_workflow_definition/cwl/__main__.py

@@ -27,6 +27,12 @@ def convert_argument(arg):
         for arg in argument_lst
         if "--function=" in arg
     ][0]
+    file = [
+        load_function(funct=arg.split("=")[-1])
+        for arg in argument_lst
+        if "--workflowfile=" in arg
+    ][0]
+    shutil.copyfile(file, os.curdir)
     kwargs = {
         arg.split("=")[0][6:]: convert_argument(arg=arg.split("=")[-1])
         for arg in argument_lst

python_workflow_definition/src/python_workflow_definition/cwl/export.py

@@ -98,18 +98,18 @@ def _write_function_cwl(workflow):
                 },
                 "workflowfile": {
                     "type": "File",
-                    "inputBinding": {"position": 2},
+                    "inputBinding": {"position": 2, "prefix": "--workflowfile=", "separate": False},
                     "default": {"class": "File", "location": "workflow.py"},
                 },
             },
             "outputs": {},
         }
-        template["inputs"]["workflowfile"]["default"]["location"] = (
-            function_nodes_dict[i].split(".")[0] + ".py"
-        )
         file_name = function_nodes_dict[i].split(".")[-1] + ".cwl"
         if file_name not in file_lst:
             file_lst.append(file_name)
+            template["inputs"]["workflowfile"]["default"]["location"] = (
+                function_nodes_dict[i].split(".")[0] + ".py"
+            )
             template["inputs"].update(
                 _get_function_template(function_name=function_nodes_dict[i])
             )