[MISC] Replace execution_handler with OpenMP #539
Workflow file for this run
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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-13" | |
| build_type: Release | |
| cxx_flags: "-std=c++23" | |
| - name: "CWL" | |
| compiler: "gcc-13" | |
| build_type: Release | |
| cxx_flags: "-std=c++23" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| path: raptor | |
| fetch-depth: 2 | |
| submodules: true | |
| - name: Setup toolchain | |
| uses: seqan/actions/setup-toolchain@main | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| ccache_size: 150M | |
| - name: Install CMake | |
| uses: seqan/actions/setup-cmake@main | |
| with: | |
| cmake: 3.25.3 | |
| - name: Install Nextflow | |
| if: matrix.name == 'Nextflow' | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: latest-stable | |
| - name: Install cwltool | |
| if: matrix.name == 'CWL' | |
| run: | | |
| install pipx | |
| pipx install cwltool | |
| - name: Configure Raptor | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \ | |
| -DHIBF_NATIVE_BUILD=OFF | |
| - name: Build Raptor | |
| run: | | |
| ccache -z | |
| cd build | |
| make -k -j2 | |
| make install | |
| ccache -sv | |
| - name: Run Nextflow | |
| if: matrix.name == 'Nextflow' | |
| run: | | |
| cd raptor/workflow/nextflow | |
| 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 raptor/workflow/cwl/tests/raptor-build-0_bins_window_19.yml | |
| cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-16_bins_window_19.yml | |