snakedeploy_tests.yaml

name: Snakedeploy

on:
  push:
  pull_request:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}

jobs:
  snakedeploy_tests:
    env:
        THREADS: 5

    strategy:
      max-parallel: 5
      fail-fast: false
      matrix:
         virus: ["hiv", "sars-cov-2"]

    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout test data
        uses: actions/checkout@v4
        with:
            sparse-checkout: |
                tests
                resources/*/gffs
            sparse-checkout-cone-mode: false
            lfs: false
            # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS

      - name: Install conda environment dependencies
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          miniforge-variant: Miniforge3
          python-version: "3.11" # temporary fix for snakemake issue #2480
          mamba-version: "*"
          use-mamba: true
          no-implicit-channels: true
          channels: conda-forge,bioconda
          channel-priority: strict
          activate-environment: snakemake
          auto-update-conda: true
          environment-file: tests/conda_snakedeploy_env.yaml

      - name: Snakedeploy
        # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out
        run: |
            snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)"

      - name: Configure
        run: |
            tests/configure_for_virus.sh "${{ matrix.virus }}"

            # HACK: currently remote URL aren't supported as directories
            cp -vrf "resources/${{ matrix.virus }}/gffs" ./

      - name: Run test
        run: |
            PYTHONUNBUFFERED=1 snakemake \
                --config "input={gff_directory: 'gffs'}" \
                --use-conda \
                --cores "${THREADS}" \
                --dry-run

            echo
            cat config/samples.tsv
            echo

            PYTHONUNBUFFERED=1 snakemake \
                --config "input={gff_directory: 'gffs'}" \
                --use-conda \
                --cores "${THREADS}" \
                -p \
                --keep-going

      - name: Archive test results
        if: ${{ success() }} || ${{ failure() }}
        uses: actions/upload-artifact@v4
        with:
          name: test_output_${{ matrix.virus }}
          path: |
            ./*
            !./.git
            !./.snakemake/conda/*/
          include-hidden-files: true
          if-no-files-found: ignore