Switch to nextstrain SARS-CoV-2 gene annotation as default

[matthuska]

Nextstrain (+ maybe others?) uses an SC2 annotation where CDSs for ORF1a and ORF1b are completely non-overlapping (see nf-core/viralrecon#263). In detail:

##gff-version 3
##sequence-region MN908947 1 29903
# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
# seqname	source	feature	start	end	score	strand	frame	attribute
MN908947	GenBank	gene	266	13468	.	+	.	gene_name=ORF1a
MN908947	GenBank	gene	13468	21555	.	+	.	gene_name=ORF1b
MN908947	GenBank	gene	25393	26220	.	+	.	gene_name=ORF3a
MN908947	GenBank	gene	21563	25384	.	+	.	gene_name=S
MN908947	GenBank	gene	26245	26472	.	+	.	gene_name=E
MN908947	GenBank	gene	26523	27191	.	+	.	gene_name=M
MN908947	GenBank	gene	27202	27387	.	+	.	gene_name=ORF6
MN908947	GenBank	gene	27394	27759	.	+	.	gene_name=ORF7a
MN908947	GenBank	gene	27756	27887	.	+	.	gene_name=ORF7b
MN908947	GenBank	gene	27894	28259	.	+	.	gene_name=ORF8
MN908947	GenBank	gene	28274	29533	.	+	.	gene_name=N
MN908947	GenBank	gene	28284	28577	.	+	.	gene_name=ORF9b

We might want to switch to using the same annotation in order to align our AA mutation profiles with theirs, to make communication within the community easier.