Update vcf2maf and add stub tests #1222
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run Linting | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| NXF_VER: "24.10.1" | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| with: | |
| extra_args: "" | |
| ################### | |
| # nf-core linting # | |
| ################### | |
| # TODO Move these to pre-commit | |
| # https://github.com/nf-core/tools/pull/3141 | |
| nf-core-changes: | |
| name: nf-core-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files | |
| modules: ${{ steps.filter.outputs.modules }} | |
| modules_files: ${{ steps.module_names.outputs.result }} | |
| subworkflows: ${{ steps.filter.outputs.subworkflows }} | |
| subworkflows_files: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: | | |
| modules: | |
| - added|modified: 'modules/nf-core/**' | |
| - added|modified: 'tests/modules/nf-core/**' | |
| subworkflows: | |
| - added|modified: 'subworkflows/nf-core/**' | |
| - added|modified: 'tests/subworkflows/nf-core/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get module name | |
| uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | |
| id: module_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.modules_files }} | |
| .map(path => path | |
| .replace('modules/nf-core/', '') | |
| .split('/') | |
| .slice(0, 2) | |
| .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml') | |
| .join('/')) | |
| ) | |
| ]; | |
| - name: debug | |
| run: | | |
| echo ${{ steps.filter.outputs.modules_files }} | |
| echo ${{ steps.module_names.outputs.result }} | |
| nf-core-lint-modules: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| name: nf-core lint modules | |
| needs: nf-core-changes | |
| if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: "${{ fromJson(needs.nf-core-changes.outputs.modules_files) }}" | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| restore-keys: | | |
| ${{ runner.os }}-pip | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@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 module ${{ matrix.module }} | |
| run: nf-core modules lint ${{ matrix.module }} | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [nf-core-lint-modules] | |
| 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) }}" |