document besswarm plot fix #3437
Workflow file for this run
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| 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: | |
| Markdown: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-node@v2 | |
| - name: Install markdownlint | |
| run: npm install -g markdownlint-cli | |
| - name: Run Markdownlint | |
| run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml | |
| # If the above check failed, post a comment on the PR explaining the failure | |
| - name: Post PR comment | |
| if: failure() | |
| uses: mshick/add-pr-comment@v1 | |
| with: | |
| message: | | |
| ## Markdown linting is failing | |
| To keep the code consistent with lots of contributors, we run automated code consistency checks. | |
| To fix this CI test, please run: | |
| * Install `markdownlint-cli` | |
| * On Mac: `brew install markdownlint-cli` | |
| * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`) | |
| * Fix the markdown errors | |
| * Automatically: `markdownlint . --config .github/markdownlint.yml --fix` | |
| * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml` | |
| Once you push these changes the test should pass, and you can hide this comment :+1: | |
| We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! | |
| Thanks again for your contribution! | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| allow-repeats: false | |
| YAML: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - uses: actions/setup-node@v2 | |
| - name: Install yaml-lint | |
| run: npm install -g yaml-lint | |
| - name: Run yaml-lint | |
| run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c .github/yamllint.yml | |
| # If the above check failed, post a comment on the PR explaining the failure | |
| - name: Post PR comment | |
| if: failure() | |
| uses: mshick/add-pr-comment@v1 | |
| with: | |
| message: | | |
| ## YAML linting is failing | |
| To keep the code consistent with lots of contributors, we run automated code consistency checks. | |
| To fix this CI test, please run: | |
| * Install `yaml-lint` | |
| * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) | |
| * Fix the markdown errors | |
| * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` | |
| * Fix any reported errors in your YAML files | |
| Once you push these changes the test should pass, and you can hide this comment :+1: | |
| We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! | |
| Thanks again for your contribution! | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| allow-repeats: false | |
| 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@v1 | |
| with: | |
| python-version: "3.6" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core==1.14 | |
| - 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 ${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 |