Add Nextflow lint GitHub Actions workflow (#739)

Co-authored-by: Claude <noreply@anthropic.com>

Author: ewels

.github/workflows/nextflow-lint-comment.yml

@@ -0,0 +1,48 @@
+name: Nextflow Lint Comment
+
+on:
+  workflow_run:
+    workflows: ["Nextflow Lint"]
+    types:
+      - completed
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  comment:
+    if: github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: actions/download-artifact@v4
+        with:
+          name: lint-results
+          github-token: ${{ github.token }}
+          run-id: ${{ github.event.workflow_run.id }}
+
+      - name: Get PR info and report
+        id: pr-info
+        run: |
+          PR_NUMBER=$(cat pr-number.txt)
+          echo "pr_number=$PR_NUMBER" >> $GITHUB_OUTPUT
+          echo "comment<<EOF" >> $GITHUB_OUTPUT
+          cat report.md >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Find existing comment
+        uses: peter-evans/find-comment@v3
+        id: find-comment
+        with:
+          issue-number: ${{ steps.pr-info.outputs.pr_number }}
+          comment-author: "github-actions[bot]"
+          body-includes: "Nextflow Lint Results"
+
+      - name: Create or update PR comment
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          comment-id: ${{ steps.find-comment.outputs.comment-id }}
+          issue-number: ${{ steps.pr-info.outputs.pr_number }}
+          body: ${{ steps.pr-info.outputs.comment }}
+          edit-mode: replace

.github/workflows/nextflow-lint.yml

@@ -0,0 +1,106 @@
+name: Nextflow Lint
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Run Nextflow lint
+        run: |
+          mkdir -p lint-results
+          # TODO: Remove '|| true' to fail CI when linting errors are fixed
+          nextflow lint **/solutions/* -o json > lint-results/lint-output.json 2>&1 || true
+
+      - name: Generate markdown report
+        if: always()
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const fs = require('fs');
+            const lintOutput = JSON.parse(fs.readFileSync('lint-results/lint-output.json', 'utf8'));
+            const { summary, errors, warnings } = lintOutput;
+            const sha = context.sha;
+            const repo = `${context.repo.owner}/${context.repo.repo}`;
+
+            // Handle warnings array (added in future Nextflow version)
+            const warningsArray = warnings || [];
+            const warningCount = summary.warnings || 0;
+
+            let markdown = '**Nextflow linting complete!**\n\n';
+
+            const hasIssues = summary.errors > 0 || warningCount > 0;
+
+            if (!hasIssues) {
+              markdown += `✅ ${summary.filesWithoutErrors} files had no errors\n`;
+            } else {
+              if (summary.errors > 0) {
+                markdown += `❌ ${summary.filesWithErrors} files had ${summary.errors} errors\n`;
+              }
+              if (warningCount > 0) {
+                const filesWithWarnings = summary.filesWithWarnings || 'N/A';
+                markdown += `⚠️  ${filesWithWarnings} files had ${warningCount} warnings\n`;
+              }
+              markdown += `✅ ${summary.filesWithoutErrors} files had no errors\n\n`;
+
+              // Combine errors and warnings with type labels
+              const allIssues = [
+                ...errors.map(e => ({ ...e, type: 'Error' })),
+                ...warningsArray.map(w => ({ ...w, type: 'Warning' }))
+              ];
+
+              // Group by file
+              const grouped = {};
+              for (const issue of allIssues) {
+                if (!grouped[issue.filename]) {
+                  grouped[issue.filename] = [];
+                }
+                grouped[issue.filename].push(issue);
+              }
+
+              // Build table rows
+              const rows = [];
+              for (const [filename, fileIssues] of Object.entries(grouped).sort()) {
+                for (const issue of fileIssues) {
+                  const location = `${issue.startLine}:${issue.startColumn}`;
+                  const link = `[${filename}:${location}](https://github.com/${repo}/blob/${sha}/${filename}#L${issue.startLine})`;
+                  rows.push(`| ${issue.type} | ${link} | ${issue.message} |`);
+                }
+              }
+
+              const totalIssues = summary.errors + warningCount;
+              markdown += `<sup>💡 Tip: Click filename locations to go directly to that code.</sup>\n\n`;
+              markdown += `<details>\n<summary>View all ${totalIssues} issues</summary>\n\n`;
+              markdown += `| Type | Location | Message |\n|------|----------|---------|\n`;
+              markdown += rows.join('\n');
+              markdown += `\n\n</details>\n`;
+            }
+
+            // Write to file
+            fs.writeFileSync('lint-results/report.md', markdown);
+
+            // Add to job summary
+            await core.summary
+              .addRaw(markdown)
+              .write();
+
+      - name: Save PR info
+        if: always() && github.event_name == 'pull_request'
+        run: |
+          echo "${{ github.event.pull_request.number }}" > lint-results/pr-number.txt
+          echo "${{ github.sha }}" > lint-results/head-sha.txt
+
+      - name: Upload lint results
+        if: always() && github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: lint-results
+          path: lint-results/
+          retention-days: 1

CONTRIBUTING.md

@@ -11,6 +11,7 @@ Table of contents:
   - [Figures \& diagrams](#figures--diagrams)
   - [Content style and formatting](#content-style-and-formatting)
     - [Formatting / linting](#formatting--linting)
+    - [Nextflow linting](#nextflow-linting)
     - [Headings CI tests](#headings-ci-tests)
     - [Admonitions](#admonitions)
   - [Known limitations](#known-limitations)
@@ -137,6 +138,17 @@ Doing that produces cleaner diffs for future code reviews.
 The sentences will still be rendered as a continuous paragraph.
 For an example, have a look at the code for this paragraph.
 
+### Nextflow linting
+
+This repository uses `nextflow lint` to check Nextflow scripts for errors and warnings.
+The linter runs automatically in CI and posts results as a PR comment.
+
+To run locally:
+
+```bash
+nextflow lint .
+```
+
 ### Headings CI tests
 
 This repository includes a Python tool to validate markdown heading numbering consistency across training materials.