parameters = {'INPUT': QgsProcessingFeatureSourceDefinition(layer1.id(), True),
              'OVERLAY': QgsProcessingFeatureSourceDefinition(layer2.id(), True),
              'OUTPUT': 'memory:'}
differenced = processing.run('qgis:difference', parameters)

QgsProject.instance().addMapLayer(layer1, False)
QgsProject.instance().addMapLayer(layer2, False)

diff = processing.runalg("qgis:difference", layer1, layer2, False, None)
result = processing.getObject(diff['OUTPUT'])
# if you want to save it to file
_writer = QgsVectorFileWriter.writeAsVectorFormat(result, 'output_layer.shp', "utf-8", None, "ESRI Shapefile")