trace in debug

cwltool/provenance.py

@@ -845,7 +845,7 @@ def add_data_file(
         else:
             # This still shows up when no_listing
             _logger.debug("[provenance] File: %s", str(from_fp))
-            traceback.print_stack()
+            _logger.debug(traceback.print_stack())
         _logger.debug("[provenance] Added data file %s", path)
         if timestamp is not None:
             createdOn, createdBy = self._self_made(timestamp)

tests/wf/directory_no_listing_nested.cwl

@@ -0,0 +1,81 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+doc: >
+    Inspect provided directory and return filenames.
+    Generate a new directory and return it (including content).
+
+hints:
+  - class: DockerRequirement
+    dockerPull: docker.io/debian:stable-slim
+
+inputs:
+    dir:
+        type: Directory?
+        loadListing: no_listing
+    ignore:
+        type: Directory?
+        loadListing: no_listing
+    ignore_no_info:
+        type: Directory?
+        loadListing: no_listing
+
+
+steps:
+    ls:
+        in:
+            dir: dir
+            ignore: ignore
+        out:
+            [listing]
+        run:
+            class: CommandLineTool
+            baseCommand: ls
+            inputs:
+                dir:
+                    type: Directory
+                    inputBinding:
+                        position: 1
+                ignore:
+                    type: Directory
+                    inputBinding:
+                        position: 2
+            outputs:
+                listing:
+                    type: stdout
+
+    generate:
+        in: []
+        out:
+            [dir1]
+        run:
+            class: CommandLineTool
+            requirements:
+                ShellCommandRequirement: {}
+                LoadListingRequirement:
+                    loadListing: deep_listing
+
+            arguments:
+            - shellQuote: false
+              valueFrom: >
+                    pwd;
+                    mkdir -p dir1/a/b;
+                    echo -n a > dir1/a.txt;
+                    echo -n b > dir1/a/b.txt;
+                    echo -n c > dir1/a/b/c.txt;
+            inputs: []
+            outputs:
+                dir1:
+                    type: Directory
+                    outputBinding:
+                        glob: "dir1"
+
+outputs:
+    output_1:
+        type: File
+        outputSource: ls/listing
+    output_2:
+        type: Directory
+        outputSource: generate/dir1
+