test-build.yml

name: test-build

on: pull_request

jobs:
  run-workflow:
    runs-on: ubuntu-latest
    steps:

      - name: Checkout repository
        uses: actions/checkout@v2

      - id: auth
        name: Set up Google Cloud authentication
        uses: google-github-actions/auth@v2
        with:
          credentials_json: ${{ secrets.GOOGLE_CREDENTIALS }}

      - name: Set up Google Cloud SDK
        uses: google-github-actions/setup-gcloud@v2
        with:
          version: '>= 363.0.0'

      - name: Check gcloud CLI
        run: gcloud info

      - name: Restore results cache
        uses: actions/cache/restore@v3
        with:
          path: build/malariagen_data_cache
          # Change this key if you ever want to force clear the cache.
          key: results_cache_20230512

      - name: Install conda environment
        uses: mamba-org/setup-micromamba@v2
        with:
          environment-file: environment.yml
          environment-name: selection-atlas
          cache-downloads: true

      - name: Run analysis snakemake workflow
        shell: bash -l {0}
        run: |
          snakemake -c1 --configfile ci/config.yaml --snakefile workflow/analysis.smk --show-failed-logs

      - name: Run site build snakemake workflow
        shell: bash -l {0}
        run: |
          snakemake -c1 --configfile ci/config.yaml --snakefile workflow/site.smk --show-failed-logs

      - name: Save results cache
        uses: actions/cache/save@v3
        if: always()
        with:
          path: build/malariagen_data_cache
          # Change this key if you ever want to force clear the cache.
          key: results_cache_20230512