Code

Finish modernization#20

Code

Merged

genehack merged 20 commits intomainnextstrain/yellow-fever:mainfrom finish-modernization-2nextstrain/yellow-fever:finish-modernization-2Copy head branch name to clipboardNov 27, 2024

+896-161

Commits

Commits on Nov 16, 2024

• Download Nextclade dataset during ingest... [#2]

  Show description for 272d4c6
  genehack

  committed
  272d4c6

• Add / tweak bits to allow upload of ingested files to S3 [#2]

  genehack

  committed
  5f61500

• Convert nextclade workflow to download inputs from S3 [#2]

  genehack

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  12865fc

• Convert phylogenetic workflow to download inputs from S3 [#2]

  genehack

  committed
  52f3da5

Commits on Nov 20, 2024

• We have a gene-specific build so we don't need this comment [#2]

  genehack

  committed
  55daabf

• Set explicit clock rate of 2e-04 ± 1e-05 [#2]

  genehack

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  967c4e7

• Only run timetree on genome build [#2]

  genehack

  committed
  8f9dc75

• Put params in order of use [#2]

  genehack

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  5c62c7c

• Swap 'authors' -> 'full_authors' and 'abbr_authors' -> 'authors' [#2]

  Show description for e953108
  genehack

  committed
  e953108

Commits on Nov 21, 2024

• Add frequencies panel [#2]

  Show description for 8bef86e
  genehack

  committed
  8bef86e

• Filter out Chinese travel cases from 2016-ish outbreak [#2]

  genehack

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  0557dac

• Copypasta assign-colors.py and associated data from dengue [#2]

  genehack

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  6625d78

• Remove old colors file; update config [#2]

  genehack

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  84fea9b

Commits on Nov 26, 2024

• Update color_orderings for YFV [#2]

  Show description for a1ec892
  genehack

  committed
  a1ec892

• Build colors.tsv dynamically during phylo build {#2}

  genehack

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  bc41b40

• Add CI workflow and configs for ingest and phylogeny workflows [#2]

  Show description for bbd653e
  genehack

  committed
  bbd653e

• Add example data for ingest and phylogenetic CI workflows [#2]

  Show description for fd22561
  genehack

  committed
  fd22561

• Add ingest-to-phylo Github workflow [#2]

  genehack

  committed
  9d2aadb

• Update README [#2]

  genehack

  committed
  729a60f

• Clean up old cruft in nextclade workflow [#2]

  genehack

  committed
  04b92ca