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Generate subsampling config with a script #1102
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I'm afraid I'm confused as to the push here. If you were to implement weighted subsampling in |
Okay... maybe I'm catching up. The current YAML files generated by |
A stepping stone towards generating these configs via a script.
These can no longer be used with the shift to using untemplated subsampling configuration files.
This does not have any templates but does not make sense to keep around after other geographically based defaults have been removed.
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Yes, I'm planning to bridge the gap between current setup and
Fair point. Before seeing your comment (was offline on an airplane), I continued and expanded the script to cover all profiles/builds. By then, I also started thinking that the scoping of this PR isn't right. I'm not sure how where to take this PR - maybe it should wait and
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There are a few changes that don't impact functionality.
This implementation has some issues, but it's a stepping stone in the switch to use augur subsample.
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Description of proposed changes
Shift to having one subsampling configuration YAML per build.
Motivations:
{region}
templating must be lifted out of Snakemake so that a complete YAML config file can be given to the subsampling tool. Without a script, this would result in even more copy/pasting.Checklist
builds
,traits
,frequencies
)?scratch
dropped: