Race leader Geraint Thomas was among the riders impacted by the spray on stage 16 of the Tour de France ©Getty Images

Julian Alaphilippe secured his second stage victory of the Tour de France on a day where the race was briefly interrupted by a farmers’ protest and pepper spray.

The 218 kilometres route from Carcassonne to Bagnères-de-Luchon was expected to test the peloton as the race entered the Pyrenees following yesterday’s rest day.

The first test, surprisingly, on this stage 16 came after just 30 kilometres of racing.

Several hay bales were thrown across the road in front of the oncoming riders, causing the race to be halted.

Police attempted to break up the protest, with reports tear gas and pepper spray was used.

Several riders, including Britain's race leader Geraint Thomas and defending champion Chris Froome, were forced to seek treatment after the gas reportedly blew into the peloton.

After a 15 minute break racing resumed, with a large breakaway group allowed to move clear.

A protest by farmers delayed the stage while spray led to riders seeking treatment ©Getty Images
A protest by farmers delayed the stage while spray led to riders seeking treatment ©Getty Images

Belgium’s Philippe Gilbert attempted to break clear as the stage progressed but the Quick-Step Floors rider’s effort ended in dramatic circumstances when he crashed when descending the Portet d’Aspet.

Gilbert crashed over a wall and fell down a ravine before quickly re-emerging and continuing towards the end of the stage.

His chance of the stage victory had gone with the incident, with a group of 17 riders massing inside the final 30kmas the col du Portillon approached.

Britain’s Adam Yates launched an attack and crested the climb solo but crashed on the tricky descent with seven kilometres to go.

Alaphilippe caught and passed Yates to go clear to the finish, earning his second win of the race following a triumph on stage 10.

The Frenchman crossed the line in 5 hours 13min 22sec with Spain’s Gorka Izagirre and Yates ending 15 seconds down.

With no attacks among the general classification contenders, their group rolled into the finish together.

King of the Mountains leader Julian Alaphilippe won his second stage of this year's race ©Getty Images
King of the Mountains leader Julian Alaphilippe won his second stage of this year's race ©Getty Images

Thomas remains in the overall race lead with an advantage of 1min 39sec to Froome. 

The Netherlands’ Tom Dumoulin remains third at 1:50, while Slovenia’s Primož Roglič is fourth at 2:38.

The Grand Tour is due to continue tomorrow with its shortest normal stage for 30 years, a 65km mountain stage from Bagnères-de-Luchon to Saint-Lary-Soulan potentially proving explosive.

The climb of the Col de Portet could cause changes to the general classification.