Add option to select reference on per-sample basis

[jpalmer37]

In the future, there are predicted to be cases where there are multiple known groupings of isolates on a single production run. We therefore want more granular control over reference selection, ideally down to the individual isolate level.

I was thinking of maintaining support for all original input formats, while adding support for individual reference choice via a new column ("REF") in the input samplesheet.