Raise a clear error for an empty command line (#1618)

A CommandLineTool with no baseCommand, arguments, or input bindings
produces an empty command list. This was passed straight to
subprocess.Popen([]), which crashed with a raw
"IndexError: list index out of range" deep inside subprocess.

Guard the empty case in JobBase._execute and raise a WorkflowException
with an actionable message instead. The existing handler turns this
into a clean permanentFail rather than an unhandled traceback.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: arimu1

cwltool/job.py

@@ -307,6 +307,12 @@ def stderr_stdout_log_path(
             stderr_path = stderr_stdout_log_path(self.base_path_logs, self.stderr)
             stdout_path = stderr_stdout_log_path(self.base_path_logs, self.stdout)
             commands = [str(x) for x in runtime + self.command_line]
+            if not commands:
+                raise WorkflowException(
+                    "Cannot run a CommandLineTool that produces an empty command line. "
+                    "Specify a 'baseCommand', 'arguments', and/or an input with an "
+                    "'inputBinding' so there is a program to execute."
+                )
             if runtimeContext.secret_store is not None:
                 commands = cast(
                     list[str],

tests/test_examples.py

@@ -990,6 +990,15 @@ def test_glob_expr_error(tmp_path: Path) -> None:
     assert "Resolved glob patterns must be strings" in stderr
 
 
+def test_empty_command_line_error() -> None:
+    """A CommandLineTool with an empty command line fails cleanly, not with an IndexError."""
+    error_code, _, stderr = get_main_output([get_data("tests/wf/no-basecommand.cwl")])
+    assert error_code != 0
+    stderr = re.sub(r"\s\s+", " ", stderr)
+    assert "empty command line" in stderr
+    assert "IndexError" not in stderr
+
+
 def test_format_expr_error() -> None:
     """Better format expression error."""
     error_code, _, stderr = get_main_output(

tests/wf/no-basecommand.cwl

@@ -0,0 +1,8 @@
+#!/usr/bin/env cwl-runner
+# Regression fixture for https://github.com/common-workflow-language/cwltool/issues/1618
+# A CommandLineTool with no baseCommand/arguments/input bindings produces an empty
+# command line; running it should fail with a clear error, not a raw IndexError.
+cwlVersion: v1.2
+class: CommandLineTool
+inputs: []
+outputs: []