Improving configs for OpenMS dev and DIANN versions over 1.8.1 #4
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| name: Fork-specific CI for test_latest_dia | |
| # Trigger only for your fork and the 'test_latest_dia' test profile | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| branches: | |
| - dev | |
| paths: | |
| - "**.yml" | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run test_latest_dia with Docker | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| TEST_PROFILE: test_latest_dia | |
| EXEC_PROFILE: docker | |
| # Ensure this workflow only runs for your fork | |
| if: ${{ github.repository == 'ypriverol/quantms' }} | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "24.04.2" # Or the Nextflow version you prefer | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ secrets.GHCR_USERNAME }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Run test_latest_dia with Docker | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --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 }} | |
| 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 }}_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 }}.log | |
| include-hidden-files: true | |
| path: .nextflow.log | |
| overwrite: false |