Reorganize config and rules around filter/subsampling #185
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The wording is a bit confusing since it is a mix of inclusive and exclusive. Easier to just let the reader look at the arguments passed to augur filter, which removes the need to update a list of filters in the docstring over time.
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Subsampling is a form of filtering, but there is a conceptual distinction that is apparent in the rules and configs used in the ncov workflow, which I've mirrored here. Put all filtering-related rules in a "filter" config, which configures a rule with the same name. Put all subsampling-related rules in a "subsampling" config which also configures a rule with the same name.
Removing unnecessary sequence I/O should improve workflow run times.
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corneliusroemer
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Sep 22, 2023
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Thanks, that makes sense! |
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Description of proposed changes
Subsampling is a form of filtering, but there is a conceptual distinction that is apparent in the rules and configs used in the ncov workflow, which I've mirrored here.
Put all filtering-related rules in a "filter" config, which configures a rule with the same name.
Put all subsampling-related rules in a "subsampling" config which also configures a rule with the same name.
Related issue(s)
Follow-up to #171
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