connect nf-test data modules branch #16
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| name: Test nf-core Modules | |
| on: | |
| push: | |
| branches: | |
| - 'github_actions_mza' | |
| pull_request: | |
| workflow_dispatch: | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| discover-modules: | |
| name: Discover nf-core Modules with Tests | |
| runs-on: ubuntu-latest | |
| outputs: | |
| module_list: ${{ steps.get-modules.outputs.module_list }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| - name: List nf-core Modules with Tests | |
| id: get-modules | |
| run: | | |
| modules=$(find modules/nf-core -type d -maxdepth 1 -mindepth 1 | while read module; do | |
| if [ -d "$module/tests" ]; then | |
| basename "$module" | |
| fi | |
| done | jq -R -s -c 'split("\n")[:-1]') | |
| if [ -z "$modules" ] || [ "$modules" == "[]" ]; then | |
| echo "No modules with tests found!" | |
| exit 1 | |
| fi | |
| echo "module_list=${modules}" >> $GITHUB_OUTPUT | |
| shell: bash | |
| test-modules: | |
| needs: discover-modules | |
| runs-on: ubuntu-latest | |
| container: | |
| image: nfcore/tools:latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJson(needs.discover-modules.outputs.module_list) }} | |
| name: Test nf-core Module ${{ matrix.module }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install nf-test data | |
| run: | | |
| # Create a directory for nf-test data | |
| mkdir -p /nf-test-data | |
| # Clone the nf-core/test-datasets repository | |
| git clone https://github.com/nf-core/test-datasets.git --single-branch --branch modules /nf-test-data/test-datasets | |
| # Set environment variable for nf-test to use this data | |
| echo "NF_TEST_DATA=/nf-test-data/test-datasets" >> $GITHUB_ENV | |
| - name: Run nf-test for ${{ matrix.module }} | |
| run: | | |
| echo "Testing module: ${{ matrix.module }}" | |
| nf-test test --module ${{ matrix.module }} | |
| - name: Upload test results | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: nf-test-results-${{ matrix.module }} | |
| path: .nf-test/ |