troubleshooting nf-test #88
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| name: Test nf-core Modules | |
| on: | |
| push: | |
| branches: | |
| - 'github_actions_mza' | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: 'Runners to test on' | |
| type: choice | |
| options: | |
| - 'ubuntu-latest' | |
| - 'self-hosted' | |
| default: 'ubuntu-latest' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NFT_VER: '0.9.2' | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| NXF_VER: '24.10.1' | |
| 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") | map(select(length > 0))') | |
| if [ "$modules" == "[]" ]; then | |
| echo "No modules with tests found!" | |
| exit 1 | |
| fi | |
| echo "module_list=$modules" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Display discovered modules | |
| run: | | |
| echo "Discovered modules with tests:" | |
| echo '${{ steps.get-modules.outputs.module_list }}' | jq . | |
| shell: bash | |
| nf-test: | |
| needs: discover-modules | |
| runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJson(needs.discover-modules.outputs.module_list) }} | |
| profile: [singularity, docker, conda] | |
| name: '${{ matrix.profile }} | ${{ matrix.module }}' | |
| env: | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| steps: | |
| - name: Clean Workspace | |
| run: | | |
| rm -rf $GITHUB_WORKSPACE/* | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| with: | |
| profile: ${{ matrix.profile }} | |
| module: ${{ matrix.module }} | |
| - name: Display Test Summary | |
| if: always() | |
| run: | | |
| echo "Test Summary for ${{ matrix.module }} (${{ matrix.profile }}):" | |
| cat modules/nf-core/${{ matrix.module }}/test.tap | grep -E '^(not )?ok' | |
| shell: bash |