Important! Template update for nf-core/tools v2.11 #798
Workflow file for this run
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
| # 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)" >> "$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) }}"] | |
| exclude: | |
| - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9" | |
| - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be" | |
| - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@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@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - 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: 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 |