Problem

Fixes #1618.

A CommandLineTool with no baseCommand, arguments, or input bindings produces an empty command line. cwltool passed that empty list straight to subprocess.Popen([]), which crashes with a raw, confusing error:

IndexError: list index out of range

…originating deep inside subprocess (executable = args[0]), rather than a clean validation error for the malformed-but-parseable document.

Repro

cwlVersion: v1.2
class: CommandLineTool
inputs: []
outputs: []

$ cwltool missing.cwl --debug
...
IndexError: list index out of range

Fix

Guard the empty-command case in JobBase._execute (cwltool/job.py) right after the command list is constructed, and raise a WorkflowException with an actionable message:

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.

The condition is if not commands:, so it only fires when there is genuinely nothing to execute — i.e. no container runtime wrapper (docker run …) and no command. A container job (where runtime supplies docker run <image>) is unaffected, so relying on an image's default CMD still works. The existing except WorkflowException handler turns this into a clean permanentFail instead of an unhandled traceback.

Tests

Added tests/wf/no-basecommand.cwl fixture and test_empty_command_line_error in tests/test_examples.py, asserting a non-zero exit, the new message in stderr, and no IndexError.

$ python -m pytest tests/test_examples.py::test_empty_command_line_error -q
1 passed

Verified black, flake8, and isort are clean on the changed files, and that a normal tool (tests/echo.cwl) still runs.

This change was produced with the assistance of Claude Code (model: Claude Opus). The diff, root-cause analysis, and test were reviewed by a human before submission.