ci.yaml

name: CI

on:
  - push
  - pull_request

jobs:
  ingest:
    # strategy:
    #   matrix:
    #     runtime: [docker, conda]
    # permissions:
    #   id-token: write
    name: nextstrain build ingest
    uses: ./.github/workflows/pathogen-repo-ci.yaml
    with:
      build-target: ingest
      build-args: --config viruses="hku1"
  phylogenetic:
    name: nextstrain build phylogenetic
    runs-on: ubuntu-latest
    needs: ingest
    steps:
      - name: download
        uses: actions/download-artifact@v4
        with:
          # hard-coding this for the moment...
          name: outputs-conda
          #path: ${{ github.repository }}/outputs-conda.zip
      - name: DEBUG
        run: ls -R
      - name: expand archive
        run: |
          unzip -of ${{ github.repository }}/outputs-conda.zip 'results/*' -d ingest
          rm ${{ github.repository }}/outputs-conda.zip
      - name: nextstrain build phylogenetic
        uses: ./.github/workflows/pathogen-repo-ci.yaml
        with:
          build-target: phylogenetic
          build-args: --config viruses="hku1"