Function run_cmd

plugins/ngs-analysis/scripts/ngs_run_utils.py:134–168

(cmd: list[str], cwd: Path, timeout: int | None = None)

def run_cmd(cmd: list[str], cwd: Path, timeout: int | None = None) -> dict[str, Any]:
    started = now_iso()
    try:
        result = subprocess.run(
            cmd,
            cwd=cwd,
            check=False,
            stdout=subprocess.PIPE,
            stderr=subprocess.STDOUT,
            text=True,
            timeout=timeout,
            env=_effective_env(),
        )
        output = result.stdout or ""
        return {
            "cmd": cmd,
            "cwd": str(cwd),
            "started_at": started,
            "finished_at": now_iso(),
            "returncode": result.returncode,
            "ok": result.returncode == 0,
            "stdout_tail": output[-12000:],
        }
    except subprocess.TimeoutExpired as exc:
        output = exc.stdout if isinstance(exc.stdout, str) else ""
        return {
            "cmd": cmd,
            "cwd": str(cwd),
            "started_at": started,
            "finished_at": now_iso(),
            "returncode": None,
            "ok": False,
            "error": f"TimeoutExpired: exceeded {timeout}s",
            "stdout_tail": output[-12000:],
        }


def run_cmd_stdout_to_file(