#!/usr/bin/env python3
"""
RNA-Seq DE Skill Runner
RNA-seq 差异表达分析技能执行器
"""

import argparse
import json
from datetime import datetime
from pathlib import Path


def main():
    parser = argparse.ArgumentParser(description="RNA-Seq DE Skill")
    parser.add_argument("--input-dir", required=True, help="Input directory with count matrix")
    parser.add_argument("--output-dir", required=True, help="Output directory")
    parser.add_argument("--prefix", default="", help="Output file prefix")
    parser.add_argument("--config", help="Config file (YAML)")
    parser.add_argument("--demo", action="store_true", help="Demo mode")
    
    args = parser.parse_args()
    
    print(f"RNA-Seq DE Skill v1.0.0")
    print(f"Input: {args.input_dir}")
    print(f"Output: {args.output_dir}")
    print(f"Prefix: {args.prefix}")
    
    # TODO: 实现完整的 skill 逻辑
    # 目前 skill 框架已创建，实际逻辑复用 apps/cli/run_rnaseq_de.py
    
    print("✅ RNA-Seq DE Skill 框架已就绪")
    print("实际分析请使用: apps/cli/run_rnaseq_de.py")


if __name__ == "__main__":
    main()