Cosmic rays are an essential ingredient in the evolution of the interstellar medium, as they dominate the ionisation of the dense molecular gas, where stars and planets form. However, since they are efficiently scattered by the galactic magnetic fields, many questions remain open, such as where exactly they are accelerated, what is their original energy spectrum, and how they propagate into molecular clouds. In this work we present new observations and discuss in detail a method that allows us to measure the cosmic ray ionisation rate towards the molecular clouds close to the W28 supernova remnant. To perform these measurements, we use CO, HCO+, and DCO+ millimetre line observations and compare them with the predictions of radiative transfe...