Custom MSA in batch mode (AlphaFold2_batch.ipynb)

Hi i was trying to use custom MSA(s) in batch mode (AlphaFold2_batch.ipynb). But there is no upload option. Does it work if the .a3m files are provided in the input directory as the first sequence should be treated as the query? 

And also: is it possible to reduce the clustered:extra sequences cap / max_msa of a custom uploaded msa ?