updated process to find the nf-core modules #2
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| name: Test nf-core Modules | ||
| on: | ||
| push: | ||
| branches: | ||
| - "github_actions_mza" | ||
| workflow_dispatch: | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| NXF_ANSI_LOG: false | ||
| NFT_VER: "0.9.2" # nf-test version | ||
| jobs: | ||
| discover-modules: | ||
| name: Discover nf-core Modules | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| module_list: ${{ steps.get-modules.outputs.module_list }} | ||
| steps: | ||
| - name: Checkout Code | ||
| uses: actions/checkout@v4 | ||
| - name: List nf-core Modules | ||
| id: get-modules | ||
| run: | | ||
| modules=$(find modules -type d -maxdepth 1 -mindepth 1 -exec basename {} \;) | ||
| echo "::set-output name=module_list::${modules// /,}" | ||
| shell: bash | ||
| test-modules: | ||
| needs: discover-modules | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| module: [${{ fromJSON(needs.discover-modules.outputs.module_list) }}] | ||
| name: Test nf-core Module: ${{ matrix.module }} | ||
| steps: | ||
| # Clean workspace | ||
| - name: Clean Workspace | ||
| run: | | ||
| rm -rf $GITHUB_WORKSPACE/* | ||
| # Checkout Code | ||
| - name: Checkout Code | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| # Install Nextflow | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "24.10.1" | ||
| # Run nf-test for the module | ||
| - name: Run nf-test for ${{ matrix.module }} | ||
| run: | | ||
| echo "Testing module: ${{ matrix.module }}" | ||
| nf-test --module ${{ matrix.module }} | ||
