Vipr3: Reformat input reference

[andreas-wilm]

Users tried to input files with empty first lines, windows newline etc. Fails then cryptically either at Mummer or simple_contig_joiner step. Could be avoided by creating a local, reformatted reference

Andreas

[andreas-wilm]

Unclear which tool to use that doesn't introduce unnecessary dependencies.

Could instead either check reference as first step or run mapping/input-ref before mummer/assembly (problem if faidx is more tolerant than mummer)