Add reference genome to alignment metrics

[JRWallace]

Only relevant for the Picard tools metrics, add the reference genome as an additional field in the .json file.

[JRWallace]

Might want to parse this from the Picard tools file itself -- if we use the refchef references we can use the 'key' as the reference ID, it will always be the 3rd to last entry in the path (so like, key/primary/reference.fasta).