Add parameter for specifying merge order and test with integrated ScPCA data

[allyhawkins]

Originally posted in AlexsLemonade/scpca-nf#275, we want to be able to incorporate the addition of auto.merge or randomizing the order of libraries prior to integration. However, we've never actually tested this parameter or used it. We should add that as a parameter to the workflow here and then re-run using the ScPCA datasets as the input so that we can generate reports with changes in integration order and evaluate if the integration order changes the results.