phylogenetic.yaml

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:
  workflow_call:
    inputs:
      image:
        description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")'
        required: false
        type: string

  workflow_dispatch:
    inputs:
      image:
        description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")'
        required: false
        type: string

jobs:
  phylogenetic:
    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 }}
      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/