Colibri & Apalis modules provide at least 4x PWM channels. Please check if the maximum frequency output / resolution of these built-in PWMs are sufficient for your application. Please check the appropriate Colibri or Apalis module datasheet for details about the PWM functionality.
An external chip may be used to obtain more PWM channels with higher frequency output and/or higher resolution. Alternatively, a low cost microcontroller with built-in high frequency/resolution PWM may be interfaced to a Colibri or Apalis module - e.g. via I2C, SPI, or UART.