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Add GitHub Action for Nextclade annotations #158
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Commits on Mar 25, 2024
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Prototype GitHub Action for Nextclade annotations
Adds rules, config, and GitHub Action file to support running Nextclade on all available sequences. Not yet tested.
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Commits on Mar 26, 2024
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Simplify Nextclade build config
Remove unnecessary configuration parameters from the Nextclade build config and update the workflow to allow these parameters to be missing. Since Snakemake evaluates the Python code in each rule's inputs, outputs, and params, rules that we don't plan to run in the workflow can produce key errors when their config parameters are not defined.
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Simplify Nextclade dataset logic
Simplifies the logic to get Nextclade datasets by following the same pattern as the flu_frequencies workflow [1] where we grab the default dataset for a given lineage and segment instead of specifying a reference name. The "broad" and more recent references for H3N2 HA, for example, are not too different from each other, but the Nextclade annotations for the former are far more verbose than for the latter. We also want the files produced by this workflow to plug directly into the flu_frequencies workflow logic, so it is best to use the same approach here. [1] https://github.com/nextstrain/flu_frequencies/blob/6e4298fac3361f4a6751d85bcb963064dbb9eee1/Snakefile#L95
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Adds NA to list of segments, since we want to know the subclade annotations for NA as well as HA and use these data to estimate frequencies.
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Add temporary trigger for Nextclade workflow on PR event. This should trigger the workflow when I push the update to the PR. If it works, I should drop this commit again.
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The workflow ran successfully, so removing this trigger.
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Commits on Mar 29, 2024
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Set Nextclade threads to a factor of 36
Reduce threads requested for Nextclade runs from 16 to 12 so we can run 3 Nextclade jobs at once (one per lineage) on a 36-core instance of AWS Batch.
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