diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml deleted file mode 100755 index 77358de..0000000 --- a/.github/workflows/linting.yml +++ /dev/null @@ -1,80 +0,0 @@ -name: nf-core linting -# This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure -# that the code meets the nf-core guidelines. -on: - push: - pull_request: - release: - types: [published] - -jobs: - EditorConfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - - uses: actions/setup-node@v2 - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - - Prettier: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - - uses: actions/setup-node@v2 - - - name: Install Prettier - run: npm install -g prettier - - - name: Run Prettier --check - run: prettier --check ${GITHUB_WORKSPACE} - - nf-core: - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - uses: actions/setup-python@v3 - with: - python-version: "3.6" - architecture: "x64" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core - - - name: Run nf-core lint - env: - GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - - name: Save PR number - if: ${{ always() }} - run: echo ${{ github.event.pull_request.number }} > PR_number.txt - - - name: Upload linting log file artifact - if: ${{ always() }} - uses: actions/upload-artifact@v2 - with: - name: linting-logs - path: | - lint_log.txt - lint_results.md - PR_number.txt