My colleague @rfahed and I are using the LSST Science Pipelines to perform Single Visit Processing of LSST sims produced by the Euclid Science Ground Segment.
Since our star catalogue are in units Jansky, we to convert to nJy using: convertReferenceCatalog script
The file you give above has mag_column_list containing things like TU_FNU_U_LSST: are those magnitude columns, or flux columns? The reference catalog converter assumes those are AB magnitudes, but you say above that your catalogs have units of janksy.
Actually, my colleague noticed this, and was puzzled as indeed TU_FNU_U_LSST are flux columns. Looking at the Configuration fields for the ConvertReferenceCatalogTask; it seems only AB mags are accepted. is that correct?
Yes, the basic converter only accepts AB mags to generate the flux fields. You can subclass ConvertRefcatManager and override the _getFluxes method. See ConvertGaiaManager for an example. This is noted in section 2 of the “How to” doc I linked.