Sequelize hasMany through another table

From my understanding, the tables you've created a many to many relationship and that when you query for a "Module", you want all the "Competence" associated to it.

Though I wasn't able to get .hasMany() working, the error produced was:

Trace: [TypeError: Cannot call method 'replace' of undefined]
    at null.<anonymous> (/Users/sjlu/Development/29165644/app.js:61:13)
    at tryCatch1 (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/util.js:45:21)
    at Promise._callHandler (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/promise.js:571:13)
    at Promise._settlePromiseFromHandler (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/promise.js:581:18)
    at Promise._settlePromiseAt (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/promise.js:713:18)
    at Promise._settlePromiseAt (/Users/sjlu/Development/29165644/node_modules/sequelize/lib/promise.js:76:18)
    at Promise._settlePromises (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/promise.js:854:14)
    at Async._consumeFunctionBuffer (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/async.js:85:12)
    at Async.consumeFunctionBuffer (/Users/sjlu/Development/29165644/node_modules/sequelize/node_modules/bluebird/js/main/async.js:40:14)
    at process._tickCallback (node.js:442:13)

In which this output is almost impossible to debug.

However, I was able to create your model bindings and query it correctly with the .belongsToMany() associations

Competence.belongsToMany(Module, {
    through: Module_has_competence,
    as: 'module',
    foreignKey: 'module_id'
})
Module.belongsToMany(Competence, {
    through: Module_has_competence,
    as: 'competence',
    foreignKey: 'competence_id'
})

Which outputs a query that you're looking for

  SELECT `module`.`id`, 
         `module`.`name`, 
         `module`.`description`, 
         `module`.`category_id`, 
         `module`.`module_type_id`, 
         `module`.`gives_score`, 
         `module`.`duration`, 
         `module`.`price`, 
         `module`.`createdat`, 
         `module`.`updatedat`, 
         `competence`.`id`                                  AS `competence.id`, 
         `competence`.`name`                                AS `competence.name`, 
         `competence`.`organization_id`                     AS 
         `competence.organization_id`, 
         `competence`.`competence_type_id`                  AS 
         `competence.competence_type_id`, 
         `competence`.`createdat`                           AS 
         `competence.createdAt`, 
         `competence`.`updatedat`                           AS 
         `competence.updatedAt`, 
         `competence.module_has_competence`.`id`            AS 
         `competence.module_has_competence.id`, 
         `competence.module_has_competence`.`module_id`     AS 
         `competence.module_has_competence.module_id`, 
         `competence.module_has_competence`.`competence_id` AS 
         `competence.module_has_competence.competence_id`, 
         `competence.module_has_competence`.`score`         AS 
         `competence.module_has_competence.score`, 
         `competence.module_has_competence`.`createdat`     AS 
         `competence.module_has_competence.createdAt`, 
         `competence.module_has_competence`.`updatedat`     AS 
         `competence.module_has_competence.updatedAt` 
  FROM   `module` AS `module` 
         LEFT OUTER JOIN (`module_has_competence` AS 
                         `competence.module_has_competence` 
                          INNER JOIN `competence` AS `competence` 
                                  ON `competence`.`id` = 
  `competence.module_has_competence`.`module_id`) 
  ON `module`.`id` = 
  `competence.module_has_competence`.`competence_id` 
  WHERE  `module`.`id` = 1; 

To my understanding .hasMany references a 1:M relationship, which does not require a join table.

http://docs.sequelizejs.com/en/latest/docs/associations/#one-to-many-associations

Here's the gist of how I got to this conclusion:

https://gist.github.com/sjlu/fa5c2e0e267cd692418a

Steven's answer did not work for me but switching the foreign keys.

Competence.belongsToMany(Module, {
  through: Module_has_competence,
  as: 'module',
  foreignKey: 'competence_id'
});
Module.belongsToMany(Competence, {
  through: Module_has_competence,
  as: 'competence',
  foreignKey: 'module_id'
});