Code

Add ingest#10

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Merged

kimandrews merged 17 commits intomainnextstrain/measles:mainfrom add-ingestnextstrain/measles:add-ingestCopy head branch name to clipboardFeb 14, 2024

+1,729

Commits

Commits on Feb 10, 2024

• Copy ingest from pathogen-repo-template

  Show description for 866abd6
  kimandrews

  committed
  866abd6

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

  Show description for 8555df3
  kimandrews

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  8555df3

• Add ingest config parameters

  Show description for e830f65
  kimandrews

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  e830f65

• Remove Entrez rules and config parameters

  kimandrews

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• Remove nextclade-related rules

  kimandrews

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• Remove ingest/profiles

  kimandrews

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• Add abbr_authors to metadata_columns

  kimandrews

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• Fix typo in ingest/rules/curate.smk

  kimandrews

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• Add NCBI Datasets "virus-name" field

  kimandrews

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• Remove nextclade_field_map.tsv

  kimandrews

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• Don't replace empty strain names

  kimandrews

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• Renamed "config" directory to "defaults"

  Show description for d2737ed
  kimandrews

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  d2737ed

• ingest/README.md: remove Profiles, change config to defaults

  kimandrews

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• Remove nextclade from Snakefile

  Show description for 3fb3e9e
  kimandrews

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  3fb3e9e

• Remove Entrez from docstring of fetch_from_ncbi.smk

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  90a70cd

Commits on Feb 14, 2024

• git subrepo pull (merge) --force ingest/vendored

  Show description for da3c325
  kimandrews

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  da3c325

• Update Changelog

  kimandrews

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