index.js

// Direct Imports
const express = require("express");
const winston = require("winston");

// Instantiate express
const app = express();

require("./startup/logging")();
require("./startup/middleware")(app);
// require("./startup/config")();
require("./startup/routes")(app);
require("./startup/db")();
require("./startup/validation")();

// PORT
const port = process.env.PORT || 5000;

const server = function() {
  app.listen(port, () => {
    winston.info(`Listening on port ${port}...`);
  });
}

module.exports = server;

I would wrap your server in a function.