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Add Nextclade and geo rules to example-data; disable "prM-E" build in phylo CI #24

Merged
merged 6 commits into from
Dec 5, 2024
Merged

Add Nextclade and geo rules to example-data; disable "prM-E" build in phylo CI #24

merged 6 commits into from
Dec 5, 2024

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genehack
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@genehack genehack commented Dec 2, 2024 •
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Description of proposed changes

  • Adds the Nextclade dataset and the geolocation rules TSV to ingest/example-data, making the ingest CI build independent of anything outside this repo.
  • Renames the "gene" config in phylogenetic to "builds"
  • Disables the "prM-E" build in phylogenetic CI, which should speed that step up quite a bit

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@genehack
Rename rule for copying NCBI example data for clarity [#23]
a1737c8
@genehack
Add rule to copy example Nextclade dataset data during CI [#23]
63f9e51 
Also add example Nextclade dataset ZIP file.
@genehack
Add rule to copy geolocation rules example data during CI [#23]
5522f62 
All add example geolocation rules data file.
@genehack
Rename 'gene' config to 'builds' [#22]
1e1ab27 
This provides a little more clarity into what's going on, and makes
the upcoming change of only doing the "genome" build in CI a little
easier to understand.
@genehack
Move "builds" config into defaults/config.yaml [#22]
c8739ce
@genehack
Disable "prM-E" build in phylogenetic CI [#22]
d94270f 
This build takes *far* longer to align than the whole genome build, so
disabling it should speed up the CI step quite a bit.
@genehack
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genehack commented Dec 2, 2024

The phylogenetic step of CI went from ~22 minutes to ~4. That's a win.

@genehack genehack merged commit 32afa98 into main Dec 5, 2024
5 checks passed
@genehack genehack deleted the more-example-data-23 branch December 5, 2024 04:53
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@joverlee521 joverlee521 Awaiting requested review from joverlee521

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