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Rename config to defaults #77

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7 of 12 tasks
j23414 opened this issue Jul 10, 2024 · 0 comments
Open
7 of 12 tasks

Rename config to defaults #77

j23414 opened this issue Jul 10, 2024 · 0 comments
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enhancement New feature or request

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@j23414
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j23414 commented Jul 10, 2024

Context

At some point, get through the backlog of changes to align with the latest pathogen-repo-guide.

Ingest:

  • Change authors->full_authors, abbr_authors -> authors
  • Change genbank_accession->accession, genbank_accession_rev->accession_version
  • Subsequently add code to add a generated url column
  • Perhaps, change release_date->date_released, update_date->date_updated
  • Add is_lab_host column

Phylogenetic:

  • Rename any */config to */defaults
  • Automagically filter out any is_lab_host entries from the downstream analysis
  • Update the exclude.txt if any outliers show up

Nice to have

  • Perhaps check if we can drop "set_final_strain_name.py" script by setting auspice display_defaults to 'strain' instead of 'node.name'
  • Perhaps add nextclade extensions to the auspice files
  • Perhaps add numeric clade names
  • Perhaps allow for both clade names
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Labels
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