Add ingest-to-phylogenetic GitHub Action... [#14] #34
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Note the use of pathogen-repo-build workflow requires adding the pathogen to our list of supported pathogens. See nextstrain/infra docs on how to add a new pathogen
👍 this is on my list/radar |
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Fixed both sets of file name / bucket key name issues |
Done in nextstrain/infra#27 |
...to fully automate `ingest` and subsequent rebuild of `phylogenetic` when data has changed. Includes related configuration updates, as follows: * copy github action and associated build-configs from template * customize nextstrain-automation/config.yaml files for `ingest` and `phylogenetic` builds * add custom file loading to top-level Snakefiles in `ingest` and `phylogenetic` builds * update .gitignore to ignore newly-used `phylogenetic/data` * update phylogenetic/defaults/config.yaml to remove unused keys * update values of various `metadata` and `sequences` inputs/outputs in subsidiary 'phylogenetic/rules/*.smk' files
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This was applied via a PR in the infra repo. Application: |
...to fully automate
ingestand subsequent rebuild ofphylogeneticwhen data has changed. Includes related configuration updates, as follows:ingestandphylogeneticbuildsingestandphylogeneticbuildsphylogenetic/datametadataandsequencesinputs/outputs in subsidiary 'phylogenetic/rules/*.smk' filesDescription of proposed changes
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