Fix issue of very similar runs falsely combining results in summary

[fmaguire]

If the exact same tool is run with different settings (but all the other metadata stays the same such as version) summarize falsely combines them e.g., running RGI on contigs and reads, hamronizing each output, and them combining them in a summary will end up with an interactive summary that both RGI contig and RGI-bwt results are from the same simple run of RGI.

Solution: Summarize should try and treat each file separately and assign a new config # if multiple hAMRonized files are supplied

https://github.com/pha4ge/hAMRonization/blob/master/hAMRonization/summarize.py#L16