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GPIOTE tasks will bypass GPIO operation ?

I want to generate PWM. I set timer2 events_compare[0] to toggle pin 1:

sd_ppi_channel_assign(PWM_LED_HI_CHANNEL, &(NRF_TIMER2->EVENTS_COMPARE[0]) ,&(NRF_GPIOTE->TASKS_OU    T[0]));

I set timer2 cc[3] to generate an interrupt TIMER2_IRQHandler

NRF_TIMER2->INTENSET = TIMER_INTENSET_COMPARE3_Enabled << TIMER_INTENSET_COMPARE3_Pos;

in IRQHandler, I try one of following: NRF_GPIOTE->TASKS_OUT[0] = 1;

and

nrf_gpio_pin_set(SECONDARY_LED_PIN);

Using TASKS_OUT works, but pin_set doesn't

So, If I enable GPIOTE, GPIO operation will be disabled ?

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