Feat/workflow updates #890
Workflow file for this run
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| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| name: nf-core CI | |
| on: | |
| push: | |
| branches: | |
| - "dev" | |
| pull_request: | |
| branches: | |
| - "dev" | |
| - "master" | |
| release: | |
| types: | |
| - "published" | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.8.2" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| list: | |
| name: List Tests | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| tests: ${{ steps.list.outputs.tests }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: List nf-test | |
| id: list | |
| run: | | |
| echo "tests=$(nf-test list --silent --format=json tests/pipeline/**/*.nf.test)" >> "$GITHUB_OUTPUT" | |
| test: | |
| name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: needs.list.outputs.tests != '[]' | |
| needs: [list] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| profile: ["docker"] # TODO , "singularity", "conda"] | |
| test: ["${{ fromJson(needs.list.outputs.tests) }}"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Cache Nextflow installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| 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: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v5 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda clean | |
| if: matrix.profile == 'conda' | |
| run: conda clean -a | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --profile="test,${{ matrix.profile }}" \ | |
| ${{ matrix.test }} \ | |
| --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: success() || failure() # run this step even if previous step failed | |
| with: | |
| path: ${{ matrix.test }}-${{ matrix.profile }}.xml | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml |