Use nextstrain/ingest #412
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subrepo: subdir: "vendored" merged: "1eb8b30" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "1eb8b30" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
The previous commit was created by the following command:
git subrepo clone https://github.com/nextstrain/ingest vendored
Add a section in the README on how to use this directory in the future.
Remove the copies in this repo and update references.
Both the centralized `trigger` and `trigger-on-new-data` take an owner/repo pair as the first argument.
Remove the copies in this repo and update references. Add new positional arguments required by the centralized scripts.
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Description of proposed changes
Begin usage of centralized ingest scripts and add details on how to pull new updates from the central repo.
Related issue(s)
Testing
Checks pass (Update-image failure is unrelated and can be ignored. It was triggered by a non-functional change in update-image.yml).
Run GenBank fetch and ingest on PR branch, verify successful run.
Evidence
I checked for the presence of
✅ This pipeline has successfully finished 🎉in the AWS Batch logs.I also spot checked some lines in the generated metadata file:
Run GISAID fetch and ingest on PR branch, verify successful run.
Evidence
Since I already checked an output file in the GenBank run, here I just checked for the presence of
✅ This pipeline has successfully finished 🎉in the AWS Batch logs.Post-merge: Slack notifications still work as intended.