#!/usr/bin/env python3
import configparser
import argparse
from workflow.runner import Runner

if __name__ == "__main__":
    # Collect args from the command line
    parser = argparse.ArgumentParser(description="HTS Workglow Runner v2025 ")
    parser.add_argument(
        "--config", required=True, default=False,
        help="INI config file containing workflow settings and command lines for individual steps."
    )
    args = parser.parse_args()

    # Set up Config parser for INI file
    config = configparser.ConfigParser()
    config.read( args.config )

    # tools/runner.py contains the primary path of the workflow
    # individual pieces (any of a bajillion different softwares) in bio_software/
    # Config is the content, args.config is the path.
    runner = Runner(config, args.config)
    runner.main()