move specification of reference genome from Snakefile to a config file.
Currently you need to un-comment lines or edit lines in the Snakefile
# REFERENCE GENOME
REF_SPECIES="REF SPECIES"
REF_ACCESSION="ACCESSION"
REF_ANNO_FILE="GCX_#########.#_ASM###v#_genomic"
#REF: Mtb strain H37R
#REF_SPECIES="Mycobacterium_tuberculosis_H37Rv_uid57777"
#REF_ACCESSION="NC_000962"
#REF_ANNO_FILE="GCF_000195955.2_ASM19595v2_genomic"