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Harmonize with pathogen repo guide#31

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j23414 merged 7 commits intomainnextstrain/zika:mainfrom harmonize-with-pathogen-repo-templatenextstrain/zika:harmonize-with-pathogen-repo-templateCopy head branch name to clipboardFeb 6, 2024

+4,796-129

Commits

Commits on Jan 30, 2024

• Move fetch_sequences.smk to fetch_from_ncbi.smk

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• Move transform.smk to curate.smk

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• ingest/curate: Make the field map config more user friendly

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• Harmonize ingest/config/defaults.yaml with the pathogen repo template

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• More specific naming: merging in USVI sequences

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Commits on Feb 6, 2024

• Move USVI data to the data folder

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• Update the phylogenetic data url to match ingest data url

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