Merge pull request #329 from jonasscheid/add-chromatogram-extractor #1158
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
| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |
| profile: | |
| name: Run profile tests | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "23.04.0" | |
| NXF_EDGE: "" | |
| # Test latest edge release of Nextflow | |
| - NXF_VER: "" | |
| NXF_EDGE: "1" | |
| tests: ["test_mokapot", "test_percolator", "test_ionannotator"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Uncomment only if the edge release is more recent than the latest stable release | |
| # See https://github.com/nextflow-io/nextflow/issues/2467 | |
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results | |
| # Define a second workflow only against main with additional tests: test_timstof and test_full | |
| profile_main: | |
| name: Run timsTOF profile tests | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'nf-core/mhcquant' }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "23.04.0" | |
| NXF_EDGE: "" | |
| # Test latest edge release of Nextflow | |
| - NXF_VER: "" | |
| NXF_EDGE: "1" | |
| tests: ["test_timstof"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Uncomment only if the edge release is more recent than the latest stable release | |
| # See https://github.com/nextflow-io/nextflow/issues/2467 | |
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results |