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Nextclade v3 Support #139

Merged
merged 6 commits into from
Jan 26, 2024
Merged

Nextclade v3 Support #139

merged 6 commits into from
Jan 26, 2024

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jaleezyy
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@jaleezyy jaleezyy commented Jan 25, 2024 •
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In response to error noted in #138 :

  • Added support for Nextclade v3 and associated datasets
  • Backwards compatibility maintained between v3 and v2 in both software and datasets
  • Includes fix where Nextclade version, when specified, would not update as requested
  • General performance update allowing mamba to be used when updating lineage assignment software
  • Cleaned up config.yaml for Nextclade parameters to be clearer (reflected in signalexe.py --config-only)
  • Updated dependencies for SIGNAL postprocessing

@jaleezyy jaleezyy marked this pull request as draft January 25, 2024 23:41
@jaleezyy jaleezyy self-assigned this Jan 25, 2024
@jaleezyy jaleezyy marked this pull request as ready for review January 26, 2024 04:20
@jaleezyy jaleezyy merged commit 2106195 into master Jan 26, 2024
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@jaleezyy jaleezyy deleted the nextclade3 branch February 1, 2024 16:22
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