Phylogenetic #279
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| name: 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: | |
| # This workflow will be triggered after the "Ingest" workflow has completed on the "main" branch. | |
| workflow_run: | |
| workflows: | |
| - Ingest | |
| types: | |
| - completed | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| trial_name: | |
| description: | | |
| Trial name for deploying builds. | |
| If not set, builds will overwrite existing builds at s3://nextstrain-data/hmpv* | |
| If set, builds will be deployed to s3://nextstrain-staging/hmpv_trials_<trial_name>_* | |
| required: false | |
| type: string | |
| jobs: | |
| check-new-data: | |
| if: | | |
| github.event_name == 'workflow_run' && | |
| github.event.workflow_run.conclusion == 'success' | |
| 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: | |
| # Run the workflow under two conditions | |
| # 1. `workflow_run` triggered `check-new-data` and there's new data (no cache hit) | |
| # 2. the workflow is being manually run by `workflow_dispatch` | |
| needs: [check-new-data] | |
| if: | | |
| always() && | |
| ( | |
| (needs.check-new-data.result == 'success' && needs.check-new-data.outputs.cache-hit != 'true') || | |
| github.event_name == 'workflow_dispatch' | |
| ) | |
| 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.image }} | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| run: | | |
| declare -a config | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=("deploy_url=s3://nextstrain-staging/hmpv_trials_${TRIAL_NAME}_") | |
| fi | |
| nextstrain build \ | |
| phylogenetic \ | |
| deploy \ | |
| --configfile defaults/config.yaml \ | |
| --config "${config[@]}" | |
| # 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/ |