Hypothesis: Colloidal particles in a nematic liquid crystal (NLC) exhibit very different behaviour to that observed in an isotropic medium. Such differences arise principally due to the nematic-induced elastic stresses exerted due to the interaction of NLC molecules with interfaces, which compete with traditional fluid viscous stresses on the particle. Theory: A systematic mathematical analysis of particles in an NLC microfluidic channel is performed using the continuum Beris-Edwards framework coupled to the Navier-Stokes equations. We impose strong homeotropic anchoring on the channel walls and weak homeotropic anchoring on the particle surfaces. Findings: The viscous and NLC forces act on an individual particle in opposing directions, resulting in a critical location in the channel where the particle experiences zero net force in the direction perpendicular to the flow. For multi-particle aggregation we show that the final arrangement is independent of the initial configuration, but the path towards achieving equilibrium is very different. These results uncover new mechanisms for particle separation and routes towards self-assembly. (C) 2018 Elsevier Inc. All rights reserved.