consensus calling major_cutoff knobs and defaults

[dpark01]

The major_cutoff parameter for consensus genome generation (ultimately implemented here) produces IUPAC ambiguity bases in the output assembly at positions where there is significant read support for non-major alleles. The parameter (a value from 0.0 to 1.0) defines the threshold. If the major allele frequency (the frequency of the allele with highest count) is strictly above this threshold, then a single non-ambiguous base will be called at that position. If it is equal to or below the threshold, an appropriate IUPAC ambiguity base will be chosen that represents the possible set of (2 or more) alleles seen in the alignment.

• Expose the major_cutoff knob to the outer levels of the assemble_refbased and sarscov2_illumina_full WDL workflows (they were previously only exposed at the task level).
• Change the default value of major_cutoff for both workflows to 0.75 (for sarscov2_illumina_full since it is mostly governed by contractual requirements, and for assemble_refbased because it seems to be a more sensible value than the old default of 0.5, which only calls 2-allele ambiguity codes when exact 50-50 read support is observed).