adding new tools #15
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| name: Linting | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lints: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # required for Conda | |
| shell: bash -el {0} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| - name: Cache Conda packages | |
| uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: conda-pkgs_${{ runner.os }}_${{ hashFiles('environment-dev.conda.linux-64.lock') }} | |
| - name: Set up development environment | |
| uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3.1.1 | |
| with: | |
| miniforge-version: latest | |
| conda-remove-defaults: "true" | |
| environment-file: environment-dev.conda.linux-64.lock | |
| use-only-tar-bz2: true # required for proper caching | |
| - name: Check Prettier formatting | |
| run: prettier --check . | |
| - name: Check Python script formatting | |
| run: ruff format --check bin/ | |
| - name: Lint Python scripts | |
| run: ruff check --extend-select I bin/ | |
| - name: Lint and check formatting of local Nextflow scripts | |
| run: | | |
| find main.nf workflows/ subworkflows/local modules/local \ | |
| -exec nextflow lint -format -sort-declarations -harshil-alignment {} + \ | |
| | (! grep 'formatted') \ | |
| || (echo 'Some Nextflow scripts were not formatted properly!' && exit 1) | |
| - name: Lint nf-core modules | |
| run: nf-core --hide-progress modules lint --all | |
| - name: Lint nf-core subworkflows | |
| run: nf-core --hide-progress subworkflows lint --all |