Add opt-in feature gpu
#8583
Workflow file for this run
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| name: Create a pipeline and test it | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| RunTestWorkflow: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-run-test-worfklow | |
| - runner=4cpu-linux-x64 | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.10.8" | |
| - "latest-everything" | |
| steps: | |
| - name: go to working directory | |
| run: | | |
| mkdir -p create-test-wf | |
| cd create-test-wf | |
| export NXF_WORK=$(pwd) | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| name: Check out source-code repository | |
| - name: Set up Python 3.13 | |
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: "3.13" | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ matrix.NXF_VER }} | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: "0.9.2" | |
| install-pdiff: true | |
| - name: Run nf-core/tools to create pipeline | |
| run: | | |
| mkdir create-test-wf && cd create-test-wf | |
| export NXF_WORK=$(pwd) | |
| nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" | |
| - name: copy snapshot file | |
| run: | | |
| cp ${{ github.workspace }}/.github/snapshots/default.nf.test.snap create-test-wf/nf-core-testpipeline/tests/default.nf.test.snap | |
| - name: Run nf-test | |
| shell: bash | |
| run: | | |
| cd create-test-wf/nf-core-testpipeline | |
| nf-test test \ | |
| --profile=+docker \ | |
| --verbose \ | |
| --tap=test.tap \ | |
| --ci | |
| # Save the absolute path of the test.tap file to the output | |
| echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT | |
| - name: Upload log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 | |
| with: | |
| name: nf-core-log-file-${{ matrix.NXF_VER }} | |
| path: create-test-wf/log.txt | |
| - name: Cleanup work directory | |
| # cleanup work directory | |
| run: | | |
| sudo rm -rf create-test-wf | |
| sudo rm -rf /home/ubuntu/tests/ | |
| if: always() | |
| shell: bash |