import shutil
from pathlib import Path
import yaml
from .utils import run, autodetect_amber_files, substitute_protein_pdb, make_coby_ter_pdb, insert_ssbonds_into_tleap

def run_pipeline(args):
    pdb = Path(args.input)
    base = pdb.stem

    # Example: Copy tleap.in from package data to working dir
    try:
        from importlib.resources import files
        tleap_template = files("aaby.data").joinpath("tleap.in")
        shutil.copy(tleap_template, "tleap.in")
    except Exception:
        import pkg_resources
        tleap_template = pkg_resources.resource_filename("aaby", "data/tleap.in")
        shutil.copy(tleap_template, "tleap.in")

    # ...continue the workflow as in your previous script...
    # Use run(), autodetect_amber_files(), etc as imported from utils.py
    # For brevity, you can paste your refactored logic here, calling functions for each step.
    print("Pipeline would run here. See workflow.py for extension.")

    # This is a skeleton; you can now fill in each workflow step as a function.
