Ingest to phylogenetic #10
Workflow file for this run
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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/ | |
| # 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: ${{ steps.check-cache.outputs.cache-hit }} | |
| steps: | |
| - name: Get sha256sum | |
| id: get-sha256sum | |
| run: | | |
| s3_urls=( | |
| "s3://nextstrain-data/files/workflows/zika/metadata.tsv.zst" | |
| "s3://nextstrain-data/files/workflows/zika/sequences.fasta.zst" | |
| ) | |
| for s3_url in "${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}" >> 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 | |
| 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 | |
| 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/ |