relocate schema files #120
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| name: Run tests | |
| on: | |
| pull_request: | |
| branches: [main] | |
| 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: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| # FIXME Flip this off once we get to less than a couple hundred. Adding | |
| # this so it will only run against changed files. It'll make it much | |
| # easier to fix these as they come up rather than everything at once. | |
| with: | |
| extra_args: "" | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier@3.1.0 | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose detected tags as 'workflows' output variables | |
| paths: ${{ steps.list.outputs.components }} | |
| subworkflows: ${{ steps.outputs.outputs.subworkflows}} | |
| # Prod for version bumping | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: List nf-test files | |
| id: list | |
| uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6 | |
| with: | |
| head: ${{ github.sha }} | |
| base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} | |
| n_parents: 0 | |
| - name: Select subworkflows | |
| id: outputs | |
| run: | | |
| echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/mirpedrol/"; ""))') >> $GITHUB_OUTPUT | |
| - name: debug | |
| run: | | |
| echo ${{ steps.outputs.outputs.subworkflows }} | |
| lint-changes: | |
| name: lint-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files | |
| subworkflows: ${{ steps.filter.outputs.subworkflows }} | |
| subworkflows_files: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: | | |
| subworkflows: | |
| - added|modified: 'subworkflows/mirpedrol/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get subworkflow name | |
| uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.subworkflows_files }} | |
| .map(path => path | |
| .replace('tests/', '') | |
| .replace('subworkflows/mirpedrol/', '') | |
| .split('/') | |
| .slice(0, 2) | |
| .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.test') && !x.endsWith('.snap')) | |
| .join('/')) | |
| ) | |
| ]; | |
| - name: debug | |
| run: | | |
| echo ${{ steps.filter.outputs.subworkflows_files }} | |
| echo ${{ steps.subworkflow_names.outputs.result }} | |
| nf-core-lint-subworkflows: | |
| runs-on: ubuntu-latest | |
| name: nf-core-lint-subworkflows | |
| needs: lint-changes | |
| if: ( needs.lint-changes.outputs.subworkflows_files != '[]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.lint-changes.outputs.subworkflows_files) }}"] | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint subworkflow ${{ matrix.tags }} | |
| run: nf-core subworkflows --git-remote https://github.com/mirpedrol/class-modules lint ${{ matrix.tags }} | |
| nf-test: | |
| runs-on: ubuntu-latest | |
| name: nf-test | |
| needs: nf-test-changes | |
| if: ( needs.nf-test-changes.outputs.paths != '[]' ) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] | |
| profile: [conda, docker, singularity] | |
| exclude: | |
| - profile: conda | |
| path: subworkflows/mirpedrol/msa_alignment | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.8.4" | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "24.10.2" | |
| - name: Set up Python | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: "0.9.2" | |
| install-pdiff: true | |
| - name: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| shell: bash | |
| run: | | |
| mkdir -p ${{ github.workspace }}/.singularity | |
| mkdir -p ${{ github.workspace }}/.singularity | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | |
| with: | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| conda-remove-defaults: true | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip cryptography | |
| # Test the component | |
| - name: Run nf-test | |
| shell: bash | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| run: | | |
| PROFILE=${{ matrix.profile }} | |
| NFT_WORKDIR=~ \ | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tap=test.tap \ | |
| --verbose \ | |
| ${{ matrix.path }} | |
| - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | |
| with: | |
| path: >- | |
| test.tap | |
| - name: Clean up | |
| if: always() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [prettier, editorconfig, nf-core-lint-subworkflows, nf-test-changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |