From 6f0ae648e3505b7f81fe2b428135e2c4ced39516 Mon Sep 17 00:00:00 2001
From: arimu1 <19286898+arimu1@users.noreply.github.com>
Date: Thu, 18 Jun 2026 20:09:33 +0700
Subject: [PATCH 1/2] 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>
---
 cwltool/job.py              | 6 ++++++
 tests/test_examples.py      | 9 +++++++++
 tests/wf/no-basecommand.cwl | 8 ++++++++
 3 files changed, 23 insertions(+)
 create mode 100644 tests/wf/no-basecommand.cwl

diff --git a/cwltool/job.py b/cwltool/job.py
index 9dd5b6662..06cbbb502 100644
--- a/cwltool/job.py
+++ b/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],
diff --git a/tests/test_examples.py b/tests/test_examples.py
index 28245b905..9cc9f5e25 100644
--- a/tests/test_examples.py
+++ b/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(
diff --git a/tests/wf/no-basecommand.cwl b/tests/wf/no-basecommand.cwl
new file mode 100644
index 000000000..657fda743
--- /dev/null
+++ b/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: []

From f004621a35387da33639a23a23bbd273bc3524a8 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Jun 2026 15:50:59 +0200
Subject: [PATCH 2/2] confirm that containerized tools don't trigger the empty
 commands error

---
 tests/test_examples.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/test_examples.py b/tests/test_examples.py
index 9cc9f5e25..c79f246f7 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -999,6 +999,17 @@ def test_empty_command_line_error() -> None:
     assert "IndexError" not in stderr
 
 
+@needs_docker
+def test_empty_command_line_container_noerror() -> None:
+    """A CommandLineTool with an empty command line fails cleanly, not with an IndexError."""
+    error_code, _, stderr = get_main_output(
+        ["--default-container", "debian:stable-slim", get_data("tests/wf/no-basecommand.cwl")]
+    )
+    assert error_code == 0
+    assert "empty command line" not in stderr
+    assert "IndexError" not in stderr
+
+
 def test_format_expr_error() -> None:
     """Better format expression error."""
     error_code, _, stderr = get_main_output(