Do not reset listingn in workflows

src/toil/cwl/cwltoil.py

@@ -4142,12 +4142,16 @@ def main(args: Optional[list[str]] = None, stdout: TextIO = sys.stdout) -> int:
                 # ToilFsAccess needs to be set up if we want to be able to use
                 # URLs.
                 builder = tool._init_job(initialized_job_order, runtime_context)
-
-                # make sure this doesn't add listing items; if shallow_listing is
-                # selected, it will discover dirs one deep and then again later on
-                # (probably when the cwltool builder gets ahold of the job in the
-                # CWL job's run()), producing 2+ deep listings instead of only 1.
-                builder.loadListing = "no_listing"
+                if not isinstance(tool, cwltool.workflow.Workflow):
+                    # make sure this doesn't add listing items; if shallow_listing is
+                    # selected, it will discover dirs one deep and then again later on
+                    # (when the cwltool builder gets constructed from the job in the
+                    # CommandLineTool's job() method,
+                    # see https://github.com/common-workflow-language/cwltool/blob/9cda157cb4380e9d30dec29f0452c56d0c10d064/cwltool/command_line_tool.py#L951),
+                    # producing 2+ deep listings instead of only 1.
+                    # ExpressionTool also uses a builder, see https://github.com/common-workflow-language/cwltool/blob/9cda157cb4380e9d30dec29f0452c56d0c10d064/cwltool/command_line_tool.py#L207
+                    # Workflows don't need this because they don't go through CommandLineTool or ExpressionTool
+                    builder.loadListing = "no_listing"
 
                 builder.bind_input(
                     tool.inputs_record_schema,