Use CLI argument strings in config - #60
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Added comments with general thoughts. I also added to dev chat agenda for tomorrow if you want more discussion before merging.
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Command-line parameters for filter, refine, ancestral, traits, and tip_frequencies are now defined as a single argument string under rule.build in config. This reverts "Use 'refine.build.option' pattern" (eed11d0) and provides a consistent and flexible pattern for passing non-file arguments to Augur.
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Description of proposed changes
Command-line parameters for
filter,refine,ancestral,traits, andtip_frequenciesare now defined as a single argument string under<rule>.<build>in config. This reverts #59 and provides a consistent and flexible pattern for passing non-file arguments to Augur.The pattern is described in detail here: https://gist.github.com/victorlin/bcac1061cbbd23d67cfa30359a621de1
Draft of necessary changes on NW-PaGe fork: 263ac68
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