bugfix from upstream viral-pipelines #62
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Introducing a bugfix from viral-pipelines. This version of wf_sarscov2_nextstrain_modified (and therefore wf_titan_augur_run) appear to have inherited a bug from upstream in which the
augur refineandaugur ancestralsteps were running on unmasked input instead of masked input (likeaugur treewas properly doing). This PR fixes the workflow so that all downstream augur steps are using the masked multiple sequence alignment (fasta). Unaddressed, this bug causes weird inconsistencies sometimes where masked SNPs can create phantom nodes in the tree (see partial discussion on SPHERES slack, though most of this was discussed/debugged elsewhere).