Thomas withstood repeated attacks from Romain Bardet and his AG2R La Mondiale team on the final mountain stage and had to chase back from two punctures and finish the stage with skipping gears, but still held on to the maillot jaune.
Adam Yates (Mitchelton-Scott) jumped away to win the stage, catching breakaway rider Daniel Navarro (Cofidis) just 50 metres from the finish.
Bardet took third on the stage, with Yates and Bardet finishing second and third overall.
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