Nf core template merge 2.13 (manual) #75
Workflow file for this run
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| name: riboseq CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| release: | |
| types: | |
| - published | |
| merge_group: | |
| types: | |
| - checks_requested | |
| branches: | |
| - master | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| changes: | |
| name: Find tags to test | |
| runs-on: ubuntu-latest | |
| outputs: | |
| tags: ${{ steps.get_tags.outputs.result }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Combine all tags.yml files | |
| id: get_username | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| - name: Get tags using yq | |
| id: get_tags | |
| uses: mikefarah/yq@master | |
| with: | |
| cmd: yq -e '. | keys | tojson' .github/tags.yml | |
| nf-test: | |
| name: nf-test ${{ matrix.tags }} ${{ matrix.profile }} nf-${{ matrix.NXF_VER }} | |
| needs: [changes] | |
| if: needs.changes.outputs.tags != '[]' | |
| runs-on: ubuntu-latest | |
| env: | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.10.0" | |
| - "latest-everything" | |
| tags: ${{ fromJson(needs.changes.outputs.tags) }} | |
| profile: | |
| - "docker" | |
| exclude: | |
| - tags: "custom/dumpsoftwareversions" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --verbose | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |