connect nf-test data #14
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | |
| - name: Display discovered modules | |
| run: | | |
| echo "Discovered modules with tests:" | |
| echo ${{ steps.get-modules.outputs.module_list }} | jq . | |
| 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 Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: '24.10.1' | |
| - name: Install nf-test | |
| run: | | |
| pip install nf-test | |
| nf-test --version | |
| - 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 /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/ |