[INFRA] Update CPM Packages #676
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| # SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin | |
| # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik | |
| # SPDX-License-Identifier: CC0-1.0 | |
| name: Workflows | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| pull_request: | |
| types: | |
| - unlabeled | |
| workflow_dispatch: | |
| concurrency: | |
| group: workflows-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: ${{ github.event_name != 'push' }} | |
| env: | |
| SHARG_NO_VERSION_CHECK: 1 | |
| TZ: Europe/Berlin | |
| defaults: | |
| run: | |
| shell: bash -Eeuxo pipefail {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "Nextflow" | |
| compiler: "gcc-14" | |
| - name: "CWL" | |
| compiler: "gcc-14" | |
| container: | |
| image: ghcr.io/seqan/${{ matrix.compiler }} | |
| volumes: | |
| - /home/runner:/home/runner | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| if: matrix.name == 'Nextflow' | |
| working-directory: /usr/local/bin | |
| run: | | |
| apt-get update | |
| apt-get install --yes default-jre-headless | |
| curl -s https://get.nextflow.io | bash | |
| - name: Install cwltool | |
| if: matrix.name == 'CWL' | |
| run: | | |
| apt-get update | |
| apt-get install --yes cwltool | |
| - name: Configure Raptor | |
| run: | | |
| mkdir build && cd build | |
| cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-Wno-interference-size" | |
| - name: Build Raptor | |
| working-directory: build | |
| run: | | |
| ccache -z | |
| make -k | |
| make install | |
| ccache -svvx | |
| - name: Run Nextflow | |
| if: matrix.name == 'Nextflow' | |
| working-directory: workflow/nextflow | |
| run: nextflow hibf.nf | |
| - name: Run cwltool | |
| if: matrix.name == 'CWL' | |
| run: | | |
| raptor build --export-help cwl > raptor.cwl | |
| cwltool --validate raptor.cwl | |
| cwltool raptor.cwl workflow/cwl/tests/raptor-build-0_bins_window_19.yml | |
| cwltool raptor.cwl workflow/cwl/tests/raptor-build-16_bins_window_19.yml | |