Heterodyne data from the James Clerk Maxwell Telescope consists of data taken from a backend correlator such as ACSIS or the DAS and a frontend such as HARP (Buckle et al 2009, MNRAS, 399, 1026) or the single receptor instruments (RxA3, RXW etc). The pipeline system described here works with data taken in the ACSIS file format but can reduce data taken from the DAS if the data are first converted using the gsd2acsis SMURF command (SUN/258, SUN/259, SUN/229).