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Harmonize with pathogen repo guide #22

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j23414 opened this issue Feb 7, 2024 · 1 comment · Fixed by #35
Closed
7 tasks done

Harmonize with pathogen repo guide #22

j23414 opened this issue Feb 7, 2024 · 1 comment · Fixed by #35
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enhancement New feature or request

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j23414 commented Feb 7, 2024 •
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Context

Part of updating the pathogen repos to match a golden path:

https://github.com/nextstrain/pathogen-repo-guide

To Dos

  • Rename ingest/workflow/snakemake_rules to ingest/rules
  • Rename ingest/rules/*.smk to match pathogen-repo-guide/rules/*
  • Move ingest/source-data/* files to ingest/config
  • Modernize ncbi-field-map in config
  • Add a CHANGELOG.md file
  • Rename "config" to "defaults"
  • Move nextstrain automation rules and configs to ingest/build-configs
@j23414 j23414 added the enhancement New feature or request label Feb 7, 2024
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j23414 commented Feb 7, 2024 •
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Planned to postpone the harmonization process until the subsequent pull requests were integrated to prevent any merge conflicts.

@j23414 j23414 mentioned this issue Mar 18, 2024
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@j23414 j23414 linked a pull request Mar 18, 2024 that will close this issue
Harmonize ingest with pathogen repo guide #35
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@j23414 j23414 mentioned this issue May 21, 2024
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Harmonize ingest with pathogen repo guide nextstrain/dengue
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