Ingest to phylogenetic #6
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Ingest to phylogenetic | |
| 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} | |
| 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://git.luolix.topmunity/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 5pm UTC (1pm EDT/10am PDT) since curation by NCBI happens on the East Coast. | |
| # We were running into invalid zip archive errors at 9am PDT, so hoping an hour | |
| # delay will lower the error frequency | |
| - cron: '0 17 * * *' | |
| 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 | |
| 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 \ | |
| ingest \ | |
| all \ | |
| --configfile config/config.yaml config/optional.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: ${{ vars.AWS_DEFAULT_REGION }} | |
| run: | | |
| s3_urls=( | |
| "s3://nextstrain-data/files/workflows/hmpv/metadata.tsv.gz" | |
| "s3://nextstrain-data/files/workflows/hmpv/sequences.fasta.xz" | |
| ) | |
| # Code below is modified from ingest/upload-to-s3 | |
| # https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29 | |
| no_hash=0000000000000000000000000000000000000000000000000000000000000000 | |
| for s3_url in "${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 | |
| 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 \ | |
| phylogenetic \ | |
| deploy \ | |
| --configfile defaults/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/ |