fix: integrate deployed reports with PPI KaKs handoff

apps/cli/run_rnaseq_report.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+"""Generate or open a formal RNA-seq evidence report."""
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+
+
+PROJECT_ROOT = Path(__file__).absolute().parents[2]
+if str(PROJECT_ROOT) not in sys.path:
+    sys.path.insert(0, str(PROJECT_ROOT))
+
+from gfa_core.rnaseq_report import NoSuccessfulRNASeqEvidence, generate_rnaseq_report
+
+
+def _csv(value: str) -> list[str] | None:
+    values = [item.strip() for item in str(value or "").split(",") if item.strip()]
+    return values or None
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(
+        description="Generate a deterministic formal RNA-seq result report from successful manifests."
+    )
+    parser.add_argument("--workspace", required=True, help="RNA-seq job workspace containing final/")
+    parser.add_argument("--prefix", required=True, help="RNA-seq output prefix")
+    parser.add_argument("--job-id", default="")
+    parser.add_argument("--rnaseq-scope-id", default="")
+    parser.add_argument(
+        "--expected-stages",
+        default="",
+        help="Comma-separated stages selected for the current RNA-seq batch",
+    )
+    parser.add_argument("--action", choices=("generate", "open"), default="generate")
+    parser.add_argument("--no-model", action="store_true", help="Disable optional LLM language enhancement")
+    parser.add_argument("--log-file", default="", help="Accepted for pipeline runner compatibility")
+    args = parser.parse_args()
+
+    try:
+        result = generate_rnaseq_report(
+            Path(args.workspace),
+            args.prefix,
+            rnaseq_scope_id=args.rnaseq_scope_id,
+            expected_stages=_csv(args.expected_stages),
+            use_model=not args.no_model,
+            action=args.action,
+            job_id=args.job_id,
+        )
+    except NoSuccessfulRNASeqEvidence as exc:
+        print(str(exc), file=sys.stderr)
+        return 2
+    except Exception as exc:
+        print(f"RNA-seq 结果报告生成失败：{type(exc).__name__}: {exc}", file=sys.stderr)
+        return 1
+
+    reuse = "（复用最新报告）" if result.reused else ""
+    print(
+        f"RNA-seq 结果报告已就绪{reuse}: {result.report_path} "
+        f"[coverage={result.coverage_status}, stages={','.join(result.included_stages)}]"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())