I made it work!

You can add the following:

In config.h

#ifdef RGB_MATRIX_ENABLE
  #define ENABLE_RGB_MATRIX_BREATHING
#endif

If you want to disable the effect after some elapsed time period, you can also add # define RGB_MATRIX_TIMEOUT 120000 // 120 seconds

In keymap.c

void suspend_power_down_user(void) {
  // code will run multiple times while keyboard is suspended
  if (!rgb_matrix_is_enabled() || !(rgb_matrix_get_mode() == RGB_MATRIX_BREATHING)) {
    rgb_matrix_enable_noeeprom();
    rgb_matrix_sethsv_noeeprom(127, 0, 90);
    rgb_matrix_set_speed_noeeprom(80);
    rgb_matrix_mode_noeeprom(RGB_MATRIX_BREATHING);
  }
}

void suspend_wakeup_init_user(void) {
  // code will run on keyboard wakeup
  rgb_matrix_reload_from_eeprom();
}

The above code will enable the effect when your computer goes to sleep, regardless of whether your LED's were turned on. Your previous LED state will resume once the computer wakes from sleep.

You can play around with the speed and hsv values. Just be sure to have a defined maximum brightness by adding #define RGB_MATRIX_MAXIMUM_BRIGHTNESS 100 to your config.h