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Work around issue where pyvcf writes QUAL values as '.' and not 0.
Changed
Removed the autodetect sample_id option for now.
Updated default model to be a variant calling one. Although labelled as
PromethION specific (_prom in name), this model should be preferred
on all platforms of non-variant (consensus) platform specific models.
Derive software versions from CLI rather than conda list.
Added
Field alias in sample sheet CSV serves as alternative to sample_name.