phylogenetic-ncbi.yaml

name: Phylogenetic NCBI

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
      trial-name:
        description: |
          Trial name for deploying builds.
          If not set, builds will overwrite existing builds at s3://nextstrain-data/avian-flu*
          If set, builds will be deployed to s3://nextstrain-staging/avian-flu_trials_<trial_name>_*
        required: false
        type: string

jobs:
  phylogenetic:
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      runtime: docker
      run: |
        declare -a config;

        if [[ "$TRIAL_NAME" ]]; then
          config+=(
            deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
          )
        fi;

        nextstrain build \
          . \
            deploy_all \
            --configfile config/h5n1-cattle-outbreak.yaml \
            --config "${config[@]}"

      env: |
        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
        TRIAL_NAME: ${{ inputs.trial-name }}
      artifact-name: phylogenetic-full-genome-build-output