Add nf-co2footprint plugin for emissions tracking #11767
This file contains hidden or 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: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| with: | |
| extra_args: "" | |
| ################### | |
| # nf-core linting # | |
| ################### | |
| # TODO Move these to pre-commit | |
| # https://github.com/nf-core/tools/pull/3141 | |
| nf-core-changes: | |
| name: nf-core-changes | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-changes | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| 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: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: | | |
| modules: | |
| - added|modified: 'modules/nf-core/**' | |
| subworkflows: | |
| - added|modified: 'subworkflows/nf-core/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get module name | |
| uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8 | |
| id: module_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.modules_files }} | |
| .filter(x => x.endsWith('main.nf')) | |
| .map(path => path | |
| .replace('modules/nf-core/', '') | |
| .replace(/\/main\.nf$/, '') | |
| ) | |
| )]; | |
| - name: Get subworkflow name | |
| uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.subworkflows_files }} | |
| .filter(x => x.endsWith('main.nf')) | |
| .map(path => path | |
| .replace('subworkflows/nf-core/', '') | |
| .replace(/\/main\.nf$/, '') | |
| ) | |
| )]; | |
| - name: debug | |
| run: | | |
| echo ${{ steps.filter.outputs.modules_files }} | |
| echo ${{ steps.module_names.outputs.result }} | |
| echo ${{ steps.filter.outputs.subworkflows_files }} | |
| echo ${{ steps.subworkflow_names.outputs.result }} | |
| nf-core-lint-modules: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-lint-modules | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| name: nf-core lint modules | |
| needs: nf-core-changes | |
| if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| - name: Set up Python | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: "3.13" | |
| - uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # 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@dded0888837ed1f317902acf8a20df0ad188d165 # v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Set up 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 ${{ matrix.module }} | |
| nf-core-lint-subworkflows: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-lint-subworkflows | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| name: nf-core lint subworkflows | |
| needs: nf-core-changes | |
| if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| - name: Set up Python | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: "3.13" | |
| - name: Set up 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 subworkflow ${{ matrix.subworkflow }} | |
| run: nf-core subworkflows lint ${{ matrix.subworkflow }} | |
| confirm-pass-lint: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-confirm-pass-lint | |
| - runner=2cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| needs: [nf-core-lint-modules, nf-core-lint-subworkflows] | |
| 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) }}" |