update name of general gbk ref file! - #4

It seems like the ingest/bin/generate_from_genbank.py script actually generates a file called config/reference.gbk rather than config/reference_sequence.gb as listed in the README.md and the snakefile .

Currently this causes an error when trying to run the rule extract:

MissingInputException in rule extract in file /template_nextstrain/Snakefile, line 131:
Missing input files for rule extract:
    output: whole_genome/config/reference.fasta, whole_genome/config/reference.gbk
    wildcards: seg=whole_genome
    affected files:
        config/reference_sequence.gb

Can fix by updating the snakefile to specify config/reference.gbk instead