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Fix ingest automation #4

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joverlee521 merged 2 commits into from
Aug 3, 2026
Merged

Fix ingest automation #4

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c92918e
ingest/nextstrain-automation: Fix puumalaense spelling
joverlee521 Aug 3, 2026
2d38668
Add nextstrain-pathogen.yaml
joverlee521 Aug 3, 2026
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14 changes: 7 additions & 7 deletions ingest/build-configs/nextstrain-automation/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,13 @@ files_to_upload:
htnv/m/sequences.fasta.zst: results/Orthohantavirus_hantanense/m/sequences_curated.fasta
htnv/s/metadata.tsv.zst: results/Orthohantavirus_hantanense/s/metadata_curated.tsv
htnv/s/sequences.fasta.zst: results/Orthohantavirus_hantanense/s/sequences_curated.fasta
# puumalasense
puuv/l/metadata.tsv.zst: results/Orthohantavirus_puumalasense/l/metadata_curated.tsv
puuv/l/sequences.fasta.zst: results/Orthohantavirus_puumalasense/l/sequences_curated.fasta
puuv/m/metadata.tsv.zst: results/Orthohantavirus_puumalasense/m/metadata_curated.tsv
puuv/m/sequences.fasta.zst: results/Orthohantavirus_puumalasense/m/sequences_curated.fasta
puuv/s/metadata.tsv.zst: results/Orthohantavirus_puumalasense/s/metadata_curated.tsv
puuv/s/sequences.fasta.zst: results/Orthohantavirus_puumalasense/s/sequences_curated.fasta
# puumalaense
puuv/l/metadata.tsv.zst: results/Orthohantavirus_puumalaense/l/metadata_curated.tsv
puuv/l/sequences.fasta.zst: results/Orthohantavirus_puumalaense/l/sequences_curated.fasta
puuv/m/metadata.tsv.zst: results/Orthohantavirus_puumalaense/m/metadata_curated.tsv
puuv/m/sequences.fasta.zst: results/Orthohantavirus_puumalaense/m/sequences_curated.fasta
puuv/s/metadata.tsv.zst: results/Orthohantavirus_puumalaense/s/metadata_curated.tsv
puuv/s/sequences.fasta.zst: results/Orthohantavirus_puumalaense/s/sequences_curated.fasta
# seoulense
seov/l/metadata.tsv.zst: results/Orthohantavirus_seoulense/l/metadata_curated.tsv
seov/l/sequences.fasta.zst: results/Orthohantavirus_seoulense/l/sequences_curated.fasta
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6 changes: 6 additions & 0 deletions nextstrain-pathogen.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# This file's *existence* marks the top level of a Nextstrain pathogen repo,
# which allows `nextstrain build` to be run from any subdirectory of the repo
# regardless of runtime. For more details, see
# <https://github.com/nextstrain/cli/releases/tag/8.2.0>.
---
$schema: https://nextstrain.org/schemas/pathogen/v0