Code

Persephone#28

Code

Merged

j23414 merged 28 commits intomainnextstrain/zika:mainfrom persephonenextstrain/zika:persephoneCopy head branch name to clipboardJan 19, 2024

+3,243-477

Commits

Commits on Nov 13, 2023

• Temporary copy ingest from mpox repo until using pathogen_template_repo

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• git subrepo clone (merge) https://github.com/nextstrain/ingest ingest/vendored

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• Replace mpox text and taxon id with zika

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• Remove Nextclade related rules

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• Clear pathogen specific user provided annotations and rules

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Commits on Dec 5, 2023

• NCBI Dataset field name transformations

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• Rescue fauna data processing steps that are specific to Zika

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• Ignore snakemake state dir for current and subfolders

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  committed
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• Use genbank_accession column as ID column

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• workaround to get accession links to work

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• Move phylogenetic workflow to a phylogenetic folder

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Commits on Dec 18, 2023

• Add rules for merging USVI data with NCBI GenBank ingested data.

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• Move rules for preparing sequences to its own smk file

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• Move rules for constructing phylogeny to its own smk file

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• Move rules for annotating phylogeny to its own smk file

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• Move rules for exporting auspice json to its own smk file

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• ingest: consolidate source-data with config

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• ingest: Always provide default config values

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Commits on Jan 10, 2024

• Use a rules folder for ingest to follow pathogen-repo-template

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• Update the CI workflow

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Commits on Jan 11, 2024

• Define input paths with literal path strings

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Commits on Jan 12, 2024

• Copy contributing docs from mpox

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• Simplify README instructions

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Commits on Jan 18, 2024

• Refactor post-processing script to be specific to zika strain name fixes

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• Abbreviate authors inplace instead of a separate field

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• As discussed, always use the default config

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  committed
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• Update Contributing docs

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  and

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• fixup: add docstring

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  committed
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