Global sensitivity analysis is used to quantify the influence of uncertain input parameters on the response variability of a numerical model. The common quantitative methods are appropriate with computer codes having scalar input variables. This paper aims at illustrating different variance-based sensitivity analysis techniques, based on the so-called Sobol's indices, when some input variables are functional, such as stochastic processes or random spatial fields. In this work, we focus on large cpu time computer codes which need a preliminary metamodeling step before performing the sensitivity analysis. We propose the use of the joint modeling approach, i.e., modeling simultaneously the mean and the dispersion of the code outputs using two interlinked Generalized Linear Models (GLM) or Generalized Additive Models (GAM). The "mean model" allows to estimate the sensitivity indices of each scalar input variables, while the "dispersion model" allows to derive the total sensitivity index of the functional input variables. The proposed approach is compared to some classical sensitivity analysis methodologies on an analytical function.Lastly, the new methodology is applied to an industrial computer code that simulates the nuclear fuel irradiation.