docker-compose specify how to launch containers, not how to modify an existing running container.

The Rancher documentation mentions that, for default usage of secrets, you can reference the secret by name in the secrets array in the docker-compose.yml.

The target filename will be the same name as the name of the secret. By default, the target filename will be created as User ID and Group ID 0, and File Mode of 0444.

Setting external to true in the secrets part will make sure it knows the secret has already been created.

Example of a basic docker-compose.yml:

version: '2'
services:
  web:
    image: sdelements/lets-chat
    stdin_open: true
    secrets:
    - name-of-secret
    labels:
      io.rancher.container.pull_image: always
secrets:
  name-of-secret:
    external: true

As illustrated in "How to Update a Single Running docker-compose Container", updating a container would involve a "build, kill, and up" sequence.

docker-compose up -d --no-deps --build <service_name>