Move s3_dst config to top level config #215
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Description of proposed changes
Nested configs for s3 URLs are challenging to override by the Snakemake
--config
option, as discussed in the following comment:nextstrain/dengue#13 (comment)
This moves the url to the top level as a
s3_dst
config value, and propagate those changes to the relevant Snakefiles.It's important to note that I haven't conducted thorough testing, and there may be nuances in the implementation meant by the comment. Suggestions or clarification welcome.
Additionally, I was unsure regarding whether the
s3_dst
config should be a required value or an optional default (Snakemake styleguide: config values).Related issue(s)
Checklist