In mongodb, the equivalent to a sql file is basically a js file.
See here for more info.
And just a note: mongoose is an odm, not a driver.
Update
Suppose we have the following script file
/**
* script.js
*/
db.createCollection('test');
You can execute it in mongo
shell this way:
mongo 127.0.0.1:27017/dbname ./script.js
If you need to specify a username and password, you can use -u and -p switches. (Read this for more info.)