You could use also IdePix module included in SNAP, it works on L1C TOA S2 data without applying atmospheric correction.
The Idepix Processor provides a pixel classification into properties such as clear/cloudy, land/water, snow, ice etc. The processing options/parameters as well as the underlying classification algorithms are instrument-dependent. The Idepix processor provided with the current SNAP version supports the Sentinel-2 MSI instrument as well as MODIS and Landsat-8.
You can find IdePix module under ‘Optical’ --> ‘Preprocessing’ --> ‘Masking’ --> ‘IdePix (Clouds, Land, Water, …)’ --> 'Sentinel-2 MSI’
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