Automate all-outbreaks build #44
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The existing code wasn't ever used, it was copy-paste from the our template repo as far as I can tell
Largely copied from <https://github.com/nextstrain/rabies> but simplified here into a single action. As we add more workflows to the repo I expect more complexity will be added. NOTE: there is not yet a schedule but one should be added once we're happy with behaviour.
joverlee521
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Dec 22, 2025
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| metadata.tsv.zst: results/metadata.tsv | ||
| metadata_open.tsv.zst: results/metadata_open.tsv | ||
| sequences.fasta.zst: results/sequences.fasta | ||
| alignments.fasta.zst: results/alignment.fasta | ||
| translations.zip: results/translations.zip | ||
| sequences_open.fasta.zst: results/sequences_open.fasta |
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To prevent our users from accidentally violating the PPX Data Use Terms, I'd want to keep the same pattern for PPX data on S3: the OPEN is the default and the RESTRICTED is explicitly labeled
metadata.tsv.zst: results/metadata_open.tsv
metadata_with_restricted.tsv.zst: results/metadata.tsv
sequences.fasta.zst: results/sequences_open.fasta
sequences_with_restricted.zst: results/sequences.fasta
alignment.fasta.zst: results/alignment_open.fasta
alignment_with_restricted.zst: results/alignment.fasta
translations_with_restricted.zip: results/translations.zip # note - no 'open' translations yet
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I added a note in #46 which will hopefully be sufficient until I get around to configuring the workflow properly.
jameshadfield
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Corresponding ebola PR <nextstrain/ebola#44> As per docs, this will be merged into master before I plan and apply the changes. <https://github.com/nextstrain/infra/blob/main/README.md#merging-prs-when-to-apply-changes>
jameshadfield
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Prompted by <#44 (comment)> this is here as a placeholder until we add proper configuration to the workflow
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I expect this won't work without changes to https://github.com/nextstrain/infra
I plan to merge shortly to allow testing and fixes / adding a schedule to happen on a branch