Automate the norovirus pathogen repository

[j23414]

Context

During Nextstrain office hours and DM's, there has been expressed interest in an automated norovirus pathogen pipeline.

• 2024-09-13 slack thread
• 2024-09-26 slack thread

Tasks

• Add ingest workflow Add ingest workflow #1
  • Basic data exploration for QC generated-report/norovirus
• Refactor existing rules into phylogenetic workflow Add phylogenetic workflow #5
• Add nextclade workflow Add Vp1 and Rdrp genotype annotations during ingest #2
  • temporary bypass this requirement by using the joining existing GenomeDetective results
• Update the top level README to highlight this is a WIP pathogen repo
• Add automation and push draft page to the staging site
  • follow instructions in the infra repo to add a new pathogen to the allowed automated list.
• Collect feedback from SME (subject-matter-experts)
• Push to live site

Examples

Possible solution

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