Fix workflow File defaults

cwltool/main.py

@@ -99,6 +99,7 @@
     HasReqsHints,
     adjustDirObjs,
     normalizeFilesDirs,
+    path_to_loc,
     processes_to_kill,
     trim_listing,
     versionstring,
@@ -482,11 +483,6 @@ def init_job_order(
                 job_order_object = {}
             job_order_object[shortname(inp["id"])] = inp["default"]
 
-    def path_to_loc(p: CWLFileType | CWLDirectoryType) -> None:
-        if "location" not in p and "path" in p:
-            p["location"] = p["path"]
-            del p["path"]
-
     ns: ContextType = {}
     ns.update(cast(ContextType, job_order_object.get("$namespaces", {})))
     ns.update(cast(ContextType, process.metadata.get("$namespaces", {})))

cwltool/process.py

@@ -73,6 +73,7 @@
     ensure_writable,
     get_listing,
     normalizeFilesDirs,
+    path_to_loc,
     random_outdir,
     visit_directories,
     visit_files,
@@ -428,7 +429,9 @@ def fill_in_defaults(
             if job.get(fieldname) is not None:
                 pass
             elif job.get(fieldname) is None and "default" in inp:
-                job[fieldname] = copy.deepcopy(inp["default"])
+                default = copy.deepcopy(inp["default"])
+                visit_files_directories(default, path_to_loc)
+                job[fieldname] = default
             elif job.get(fieldname) is None and "null" in aslist(inp["type"]):
                 job[fieldname] = None
             else:

cwltool/utils.py

@@ -258,6 +258,13 @@ def visit_files_directories(rec: Any, op: Callable[[CWLFileType | CWLDirectoryTy
             visit_files_directories(d, op)
 
 
+def path_to_loc(obj: CWLFileType | CWLDirectoryType) -> None:
+    """Convert a path field to a location field."""
+    if "location" not in obj and "path" in obj:
+        obj["location"] = obj["path"]
+        del obj["path"]
+
+
 def visit_field(rec: Any, field: str, op: Callable[..., Any]) -> None:
     """Apply a function to mapping with 'field'."""
     if isinstance(rec, MutableMapping):

tests/test_default_path.py

@@ -1,4 +1,5 @@
 from cwltool.load_tool import fetch_document, resolve_and_validate_document
+from cwltool.main import main
 
 from .util import get_data
 
@@ -13,3 +14,8 @@ def test_default_path() -> None:
     assert isinstance(processobj, dict)
 
     assert "cwlVersion" in processobj
+
+
+def test_workflow_step_file_default() -> None:
+    """Run a workflow step with a default File input."""
+    assert main(["--no-container", get_data("tests/wf/workflow_step_file_default.cwl")]) == 0

tests/wf/workflow_step_file_default.cwl

@@ -0,0 +1,22 @@
+cwlVersion: v1.2
+class: Workflow
+
+inputs: []
+
+steps:
+  step_with_file_default:
+    run:
+      class: CommandLineTool
+      inputs:
+        input_with_default:
+          type: File
+          default:
+            class: File
+            path: ../../README.rst
+          inputBinding: {}
+      baseCommand: sha256sum
+      outputs: []
+    in: []
+    out: []
+
+outputs: []