encryption.js

const nacl   = require('tweetnacl');
const util   = require('tweetnacl-util');
const scrypt = require('scryptsy');
const fs     = require('fs');

let password = "Node.js is cool";
let secret_msg = util.decodeUTF8("NPM is amazing!"); // function should be named "encodeUTF8", they reversed names!

// Generate the key:
let salt = nacl.randomBytes(16);
console.log("salt:", salt); // To decrypt the data later, you have to save this salt somewhere.
let N = 16384; // number of iterations
let r = 8; // Memory factor
let p = 1; // Parallelization factor
let key = scrypt(password, salt, N, r, p, nacl.secretbox.keyLength);
console.log(key);

// Encrypt the data:
let nonce = nacl.randomBytes(nacl.secretbox.nonceLength);
console.log("nonce:", nonce); // To decrypt the data later, you have to save this salt somewhere.
let encrypted = nacl.secretbox(secret_msg, nonce, key);

// Encode in Base64:
encrypted = util.encodeBase64(encrypted);

// Store encrypted data:
fs.writeFile('file.txt', encrypted, 'ascii', function(err) { // no need of utf8 with Base64
  if (err) {
    console.log(err);
  } else {
    console.log("File saved!");
  }
});

For decryption:
https://gist.github.com/authmane512/9c74b0270a4b10a5ccc202136a6b000b