The SwissFEL facility will produce coherent, ultra-bright, and ultra-short photon pulses covering a wavelength range from 0.1 nm to 7 nm, requiring an emittance between 0.18 to 0.43 mm mrad at bunch charges between 10 pC and 200 pC. In nominal operation continuous changes between these two bunch charges will be offered to the users as a tradeoff between photon power and pulse length depending on their requirements. The facility consists of an S-band RF-gun and booster and a C-band main linac, which accelerates the beam up to 5.8 GeV. Two compression chicanes will provide a nominal peak current of about 1-3 kA depending on the charge. In addition special operation setups for ultra short single mode photon pulses and large bandwidth will be available to users. In this paper different operation modes including nominal operation as well as special modes are presented and discussed in terms of machine stability requirements.