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Hi, good question:

- if it is a waste flow, then as input (this is what I would recommend); processes creating waste have this flow then as output;

- if it is a product flow (ecoinvent / SimaPro way of modeling) you need to put it as output, with a negative sign, and those processes who create waste need to have this flow as input, with a negative sign. Be aware to really put a negative sign twice, otherwise you get negative results.