remove previously masked sites (which were specific to Belgium, probably no longer an issue) and add nucleotide corresponding to S:142
@@ -87,8 +87,7 @@ mask:
# Specific sites to mask in the reference genome's coordinates.
# These are 1-indexed coordinates of sites that have been identified as prone to sequencing errors.
- # 13402, 24389 and 24390 are restricted to Belgian samples
- mask_sites: "13402 24389 24390"
+ mask_sites: "21987"
# Depending on how you define focal and contextual inputs, the same strains may
# appear in both inputs. This option tells the workflow not to throw an error
