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Start GH Action workflow for automation
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Currently just runs the ingest workflow and uploads the results
to AWS S3. Subsequent commits will add automation for the phylogenetic
workflow.
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joverlee521 committed Mar 26, 2024
1 parent 7b3fe1a commit 3489073
Showing 1 changed file with 31 additions and 0 deletions.
31 changes: 31 additions & 0 deletions .github/workflows/ingest-to-phylogenetic.yaml
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name: Ingest to phylogenetic

on:
workflow_dispatch:

jobs:
ingest:
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
# Starting with the default docker runtime
# We can migrate to AWS Batch when/if we need to for more resources or if
# the job runs longer than the GH Action limit of 6 hours.
runtime: docker
run: |
nextstrain build \
--env AWS_ACCESS_KEY_ID \
--env AWS_SECRET_ACCESS_KEY \
ingest \
upload_all \
--configfile build-configs/nextstrain-automation/config.yaml
# Specifying artifact name to differentiate ingest build outputs from
# the phylogenetic build outputs
artifact-name: ingest-build-output
artifact-paths: |
ingest/results/
ingest/benchmarks/
ingest/logs/
ingest/.snakemake/log/

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