Add new module called rundbcan and subcommands(database, cazymeannotation, easycgc, easysubstrate) #7698
Workflow file for this run
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| 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: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| with: | |
| extra_args: "" | |
| ################### | |
| # nf-core linting # | |
| ################### | |
| # TODO Move these to pre-commit | |
| # https://github.com/nf-core/tools/pull/3141 | |
| nf-core-changes: | |
| name: nf-core-changes | |
| runs-on: | |
| - runs-on=${{ 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: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: | | |
| modules: | |
| - added|modified: 'modules/nf-core/**' | |
| subworkflows: | |
| - added|modified: 'subworkflows/nf-core/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get module name | |
| uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | |
| id: module_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.modules_files }} | |
| .filter(x => x.endsWith('main.nf')) | |
| .map(path => path | |
| .replace('modules/nf-core/', '') | |
| .replace(/\/main\.nf$/, '') | |
| ) | |
| )]; | |
| - name: Get subworkflow name | |
| uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: "3.13" | |
| - uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # 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@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4 | |
| 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| 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) }}" |