--single-step can not get default value in step (#1598)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: huzech

cwltool/subgraph.py

@@ -216,7 +216,10 @@ def get_step(
 
     for inport in cast(List[CWLObjectType], step["in"]):
         name = "#" + cast(str, inport["id"]).split("#")[-1].split("/")[-1]
-        extracted["inputs"].append(CommentedMap({"id": name, "type": "Any"}))
+        inp: CWLObjectType = {"id": name, "type": "Any"}
+        if "default" in inport:
+            inp["default"] = inport["default"]
+        extracted["inputs"].append(CommentedMap(inp))
         inport["source"] = name
         if "linkMerge" in inport:
             del inport["linkMerge"]

tests/test_subgraph.py

@@ -275,6 +275,19 @@ def test_single_step_packed_subwf_step() -> None:
     )
 
 
+def test_single_with_step_level_default_value() -> None:
+    """Inherit step-level defaults with --single-step."""
+    err_code, stdout, stderr = get_main_output(
+        [
+            "--single-step",
+            "task2",
+            get_data("tests/wf/cache_test_workflow.cwl"),
+        ]
+    )
+    assert err_code == 0
+    assert "two" in stderr
+
+
 def test_print_targets_embedded_step() -> None:
     """Confirm that --print-targets works when a Workflow has embedded Processes."""
     err_code, stdout, stderr = get_main_output(