nf-core/pixelator integration tests #6
Workflow file for this run
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| #schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json | |
| name: "nf-core/pixelator integration tests" | |
| on: | |
| workflow_dispatch: | |
| env: | |
| ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f" | |
| jobs: | |
| pre_job: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| # Map a step output to a job output | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| paths_result: ${{ steps.skip_check.outputs.paths_result }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@v5 | |
| if: ${{ !env.ACT }} | |
| with: | |
| concurrent_skipping: "same_content_newer" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["workflow_dispatch"]' | |
| paths_filter: | | |
| python: | |
| paths: | |
| - 'pyproject.toml' | |
| - 'poetry.lock' | |
| - 'src/pixelator/**' | |
| - '**/Taskfile.yml' | |
| - '.github/**' | |
| paths_ignore: | |
| - 'tests/**' | |
| test: | |
| name: Test default profile | |
| if: github.event.act || needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| runs-on: ubuntu-latest | |
| needs: [pre_job] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout pixelator | |
| uses: actions/checkout@v4 | |
| - name: Checkout nf-core-pixelator | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: PixelgenTechnologies/nf-core-pixelator | |
| ref: pixelator-next | |
| path: nf-core-pixelator | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'microsoft' | |
| java-version: '21' | |
| - uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "latest-stable" | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache Conda env | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ env.CACHE_NUMBER }}--${{ hashFiles('environment.yml') }} | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache-conda | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: pixelator | |
| miniforge-version: latest | |
| channels: conda-forge,bioconda,defaults | |
| use-mamba: true | |
| environment-file: environment.yml | |
| - name: Install pixelator | |
| run: pip install -e . | |
| - name: Run nf-core/pixelator default profile with current pixelator | |
| env: | |
| PIPELINE_BRANCH: pixelator-next | |
| PIPELINE_SOURCE_DIR: ./nf-core-pixelator | |
| run: | | |
| task test-nf-core-pixelator |