Large index and genes collection option + genes collection modification

I've added options in the config file that allow the user to choose whether he want to do gene collection or not (useful if the user only wants to do co-assembly, as gene collection requires single-assembly). I've also added an option to use the bt2l extension if the number of nucleotides in the files is too high (> 4000000000). I've also put the gene collection back to its original state (clustering on predicted genes then translating into proteins).