Add STAR aligner CLI parsing and reference validation

[Fuki-Kudoh]

Motivation

• Support ADR 0001 by adding STAR as an optional alignment branch while preserving existing Salmon/kallisto behavior and CLI compatibility.
• Phase 1 scope is parser + reference validation only; STAR execution is intentionally out of scope for this PR.

Description

• Added --aligner {none,star} to the run CLI with default none, preserving legacy/omitted-flag behavior and existing --quantifier semantics (src/wulfrna/cli.py).
• Extended validate_reference() to accept aligner and to validate a star_index/ directory under the resolved reference only when --aligner star is selected, and to raise PipelineError(step="reference_check") on missing/unsupported aligner cases (src/wulfrna/pipeline.py).
• Threaded the selected aligner into the run manifest and conditionally recorded the STAR reference path when applicable (src/wulfrna/pipeline.py).
• Added pytest tests covering CLI parsing defaults and errors (tests/test_cli.py) and reference validation behavior for default/STAR/unsupported aligners (tests/test_reference_validation.py), plus tests/conftest.py to make src/ importable during tests.

Testing

• Ran pytest initially which errored due to import path issues: the run showed a ModuleNotFoundError: No module named 'wulfrna' during collection, so tests/conftest.py was added to fix imports; after that pytest passed.
• Final test runs and results:
  • pytest -> "7 passed in 0.17s".
  • python -m compileall src/wulfrna -> completed successfully (compiled package sources).
  • CLI smoke tests with mocked tool binaries (commands run inside temporary environment):
    • PATH="$tmp/bin:$PATH" PYTHONPATH=src python -m wulfrna.cli --help >/tmp/wulfrna_help.out -> help printed successfully.
    • PATH="$tmp/bin:$PATH" PYTHONPATH=src python -m wulfrna.cli run "$tmp/work" --reference "$tmp/ref" --stranded reverse --threads 4 --dry-run >/tmp/wulfrna_salmon.out -> Salmon dry-run smoke test completed successfully.
    • PATH="$tmp/bin:$PATH" PYTHONPATH=src python -m wulfrna.cli run "$tmp/work" --reference "$tmp/ref" --stranded reverse --threads 4 --quantifier kallisto --dry-run >/tmp/wulfrna_kallisto.out -> Kallisto dry-run smoke test completed successfully.
    • PATH="$tmp/bin:$PATH" PYTHONPATH=src python -m wulfrna.cli run "$tmp/work" --reference "$tmp/ref" --stranded reverse --threads 4 --aligner star --dry-run with star_index/ present -> STAR-reference validation passed.
    • Same STAR command without star_index/ -> process exited with code 1 and printed the expected error: Reference directory is missing required files: /tmp/<tmpdir>/ref/star_index (caught as PipelineError and written to status).
• All automated tests added for this change passed.

Note: package version was not changed and STAR execution was not implemented in this PR as requested.

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Codex Task

[Fuki-Kudoh]

Superseded by #16.

PR #16 incorporates the requested STAR index validation,
pytest integration, and CI updates. This PR is closed without merge
to keep a single review target.