Improving configs for OpenMS dev and DIANN versions over 1.8.1 #1211
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| 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 | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| env: | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| TEST_PROFILE: ${{ matrix.test_profile }} | |
| EXEC_PROFILE: ${{ matrix.exec_profile }} | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # Nextflow versions | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| test_profile: | |
| ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"] | |
| exec_profile: ["docker"] | |
| exclude: | |
| - test_profile: test_dia | |
| exec_profile: "conda" | |
| - test_profile: test_localize | |
| exec_profile: "conda" | |
| - NXF_VER: "latest-everything" | |
| exec_profile: "conda" | |
| include: | |
| - test_profile: test_lfq | |
| exec_profile: "conda" | |
| - test_profile: test_dda_id | |
| exec_profile: "conda" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.exec_profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.exec_profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Install micromamba | |
| env: | |
| MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba | |
| if: matrix.exec_profile == 'conda' | |
| run: | | |
| wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| echo "$(pwd)/bin" >> $GITHUB_PATH | |
| echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH | |
| ./bin/micromamba shell init -s bash | |
| echo $'channels:\n - conda-forge\n - bioconda\n - defaults\nuse_lockfiles: false' >> ~/.mambarc | |
| - name: Install Singularity with defaults | |
| if: matrix.exec_profile == 'singularity' | |
| uses: singularityhub/install-singularity@main | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data in docker/singularity profile | |
| if: matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity' | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results | |
| - name: Run pipeline with test data in conda profile (and single-threaded) | |
| env: | |
| MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba | |
| if: matrix.exec_profile == 'conda' | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results | |
| - name: Gather failed logs | |
| if: failure() || cancelled() | |
| run: | | |
| mkdir failed_logs | |
| failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2) | |
| while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed" | |
| - uses: actions/upload-artifact@v4 | |
| if: failure() || cancelled() | |
| name: Upload failed logs | |
| with: | |
| name: failed_logs_${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }} | |
| include-hidden-files: true | |
| path: failed_logs | |
| overwrite: false | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}_results | |
| include-hidden-files: true | |
| path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results | |
| overwrite: false | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload log | |
| with: | |
| name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}.log | |
| include-hidden-files: true | |
| path: .nextflow.log | |
| overwrite: false |