[phylo] Reconnect traits to export #252
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Allow users to customize the augur traits command through config params.
If there are no columns defined for `augur traits` then do not include the traits input for the `--node-data` option for `augur export`.
Restoring behavior from 43fdaf1 by providing an empty traits column config param.
genehack
reviewed
May 10, 2024
| @@ -32,9 +32,9 @@ OUTPUTS: | |||
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| rule remove_time: | |||
| input: | |||
| "results/{build_name}/branch_lengths.json", | |||
| build_dir + "/{build_name}/branch_lengths.json", | |||
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this is probably some snakemake lore i haven't absorbed yet, but i wonder: why concatenate instead of interpolate? (e.g., "{build_dir}/{build_name}/branch_lengths.json")
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Ah, this is using concatenation because the workflow uses a mix of variable (build_dir) and Snakemake wildcard (build_name) in the file paths.
We could update it to f"{build_dir}/{{build_name}}/branch_lengths.json" with double braces around build_name to keep the wildcard reference.
genehack
approved these changes
May 10, 2024
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Description of proposed changes
Reconnects the
augur traitsoutput toaugur exportbased on the presence of thetraits.columnsconfig parameter.Related issue(s)
Resolves #251
Checklist