Merge pull request #3538 from mashehu/add-py-3_13 #43
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| name: Create a pipeline from a template and test it | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| paths: | |
| - nf_core/pipeline-template/** | |
| 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 | |
| env: | |
| NXF_ANSI_LOG: false | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| prepare-matrix: | |
| name: Retrieve all template features | |
| runs-on: ubuntu-latest | |
| outputs: | |
| all_features: ${{ steps.create_matrix.outputs.matrix }} | |
| steps: | |
| - name: 🏗 Set up yq | |
| uses: frenck/action-setup-yq@c4b5be8b4a215c536a41d436757d9feb92836d4f # v1 | |
| - name: checkout | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Create Matrix | |
| id: create_matrix | |
| run: | | |
| echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT | |
| RunTestWorkflow: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-run-test-worfklow | |
| - runner=4cpu-linux-x64 | |
| needs: prepare-matrix | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} | |
| include: | |
| - TEMPLATE: all | |
| fail-fast: false | |
| steps: | |
| - name: Check out source-code repository | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - 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: latest-everything | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: "0.9.2" | |
| install-pdiff: true | |
| # Create template files | |
| - name: Create template skip ${{ matrix.TEMPLATE }} | |
| run: | | |
| mkdir create-test-lint-wf | |
| export NXF_WORK=$(pwd) | |
| if [ ${{ matrix.TEMPLATE }} == "all" ] | |
| then | |
| printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml | |
| else | |
| printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml | |
| fi | |
| # Create a pipeline from the template | |
| - name: create a pipeline from the template ${{ matrix.TEMPLATE }} | |
| run: | | |
| cd create-test-lint-wf | |
| nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml | |
| # Copy snapshot file | |
| - name: copy snapshot file | |
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | |
| run: | | |
| if [ ! -f ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap ]; then | |
| echo "Generate a snapshot when creating a pipeline and skipping the feature ${{ matrix.TEMPLATE }}." | |
| echo "Then, copy it to the directory .github/snapshots" | |
| else | |
| cp ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap | |
| fi | |
| # Run pipeline with nf-test | |
| - name: run pipeline nf-test | |
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | |
| shell: bash | |
| run: | | |
| cd create-test-lint-wf/my-prefix-testpipeline | |
| nf-test test \ | |
| --profile=+docker \ | |
| --verbose \ | |
| --ci | |
| # Remove .nf-test folder before linting | |
| - name: remove .nf-test folder | |
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | |
| run: | | |
| rm -rf create-test-lint-wf/my-prefix-testpipeline/.nf-test | |
| rm create-test-lint-wf/my-prefix-testpipeline/.nf-test.log | |
| rm create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap | |
| # Run the pipeline when nf-test is not available | |
| - name: run the pipeline | |
| if: ${{ matrix.TEMPLATE == 'all' || matrix.TEMPLATE == 'nf-test' }} | |
| run: | | |
| cd create-test-lint-wf | |
| nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results | |
| # Remove results folder before linting | |
| - name: remove results folder | |
| if: ${{ matrix.TEMPLATE == 'all' || matrix.TEMPLATE == 'nf-test' }} | |
| run: | | |
| rm -rf create-test-lint-wf/results | |
| # Try syncing it before we change anything | |
| - name: nf-core pipelines sync | |
| run: nf-core --log-file log.txt pipelines sync --dir create-test-lint-wf/my-prefix-testpipeline/ | |
| # Run code style linting | |
| - name: Run pre-commit | |
| run: pre-commit run --all-files | |
| working-directory: create-test-lint-wf | |
| # Remove TODO statements | |
| - name: remove TODO | |
| run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; | |
| working-directory: create-test-lint-wf | |
| # Uncomment includeConfig statement | |
| - name: uncomment include config | |
| run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; | |
| working-directory: create-test-lint-wf | |
| # Replace zenodo.XXXXXX to pass readme linting | |
| - name: replace zenodo.XXXXXX | |
| run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; | |
| working-directory: create-test-lint-wf | |
| # Add empty ro-crate file | |
| - name: add empty ro-crate file | |
| run: touch my-prefix-testpipeline/ro-crate-metadata.json | |
| working-directory: create-test-lint-wf | |
| # Run nf-core linting | |
| - name: nf-core pipelines lint | |
| run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned | |
| working-directory: create-test-lint-wf | |
| # Run code style linting | |
| - name: run pre-commit | |
| shell: bash | |
| run: pre-commit run --all-files | |
| working-directory: create-test-lint-wf | |
| # Run bump-version | |
| - name: nf-core pipelines bump-version | |
| run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1 | |
| working-directory: create-test-lint-wf | |
| # Run nf-core linting in release mode | |
| - name: nf-core pipelines lint in release mode | |
| run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned --release | |
| working-directory: create-test-lint-wf | |
| - name: Tar files | |
| run: tar -cvf artifact_files.tar log.txt template_skip*.yml | |
| working-directory: create-test-lint-wf | |
| - name: Upload log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 | |
| with: | |
| name: nf-core-log-file-${{ matrix.TEMPLATE }} | |
| path: create-test-lint-wf/artifact_files.tar | |
| - name: Cleanup work directory | |
| run: sudo rm -rf create-test-lint-wf | |
| if: always() |