feat: enhance pipeline examples with linting and educational highlighting

.gitignore

@@ -29,3 +29,7 @@ pnpm-debug.log*
 
 # macOS-specific files
 .DS_Store
+
+# Nextflow execution artifacts
+src/pages/examples/*/work/
+src/pages/examples/*/.nextflow*

astro.config.mjs

@@ -3,7 +3,9 @@ import { defineConfig } from "astro/config";
 import remarkDescription from "astro-remark-description";
 import remarkDirective from "remark-directive";
 import sitemap from "@astrojs/sitemap";
-import { transformerNotationDiff, transformerNotationFocus, transformerMetaHighlight } from "@shikijs/transformers";
+import expressiveCode from "astro-expressive-code";
+import { pluginLineNumbers } from "@expressive-code/plugin-line-numbers";
+import mdx from "@astrojs/mdx";
 import react from "@astrojs/react";
 import tailwind from "@astrojs/tailwind";
 
@@ -12,12 +14,6 @@ export default defineConfig({
   site: "https://nextflow.io/",
   outDir: "./output",
   markdown: {
-    shikiConfig: {
-      // Choose from Shiki's built-in themes (or add your own)
-      // https://shiki.style/themes
-      theme: "light-plus",
-      transformers: [transformerNotationDiff(), transformerNotationFocus(), transformerMetaHighlight()],
-    },
     remarkPlugins: [
       remarkDirective,
       admonitionsPlugin,
@@ -52,6 +48,8 @@ export default defineConfig({
     ],
   },
   integrations: [
+    expressiveCode(),
+    mdx(),
     react(),
     tailwind(),
     sitemap({

ec.config.mjs

@@ -0,0 +1,85 @@
+import { defineEcConfig } from "astro-expressive-code";
+import { pluginLineNumbers } from "@expressive-code/plugin-line-numbers";
+
+export default defineEcConfig({
+  // Use light theme for consistency with site design
+  themes: ["github-light"],
+
+  // Enable advanced features
+  plugins: [pluginLineNumbers()],
+
+  // Disable Expressive Code's built-in copy button and enable line numbers
+  defaultProps: {
+    showCopyToClipboardButton: false,
+    showLineNumbers: true,
+  },
+
+  // Comprehensive styling to match site's clean, minimal design
+  styleOverrides: {
+    // Core background and text styling - pure white like site
+    codeBackground: "#ffffff",
+    codeForeground: "#24292f", // GitHub light theme text color
+
+    // Typography - match site's exact monospace stack
+    codeFontFamily: "Menlo, Monaco, Consolas, 'Courier New', monospace",
+    codeFontSize: "1.25rem", // 20px - readable code size, smaller than before
+    codeLineHeight: "1.5",
+
+    // Borders - subtle gray matching site's container styling
+    borderColor: "#e5e7eb", // rgb(229, 231, 235) - light gray
+    borderWidth: "1px",
+    borderRadius: "0.375rem", // Tailwind rounded-md
+
+    // Text markers - use site's green color scheme for highlighting
+    textMarkers: {
+      // Use the site's actual light green color for highlighting
+      markBackground: "var(--nextflow-light-green)", // Direct use of site color
+      markBorderColor: "transparent", // Clean, no borders
+
+      // Make highlighting more visible but still clean
+      backgroundOpacity: "0.4", // More visible highlighting
+      borderOpacity: "0", // No border opacity
+
+      // Make text more readable on light green background
+      markForeground: "#1f2937", // Dark text for better contrast
+
+      // Label styling with bright green background
+      lineMarkerLabelColor: "#0dc09d", // Bright green for labels
+    },
+
+    // Frames - clean, minimal styling
+    frames: {
+      // Remove all shadows and heavy styling
+      shadowColor: "transparent",
+      frameBoxShadowCssValue: "none",
+
+      // Clean frame styling matching site containers
+      editorBackground: "#ffffff",
+      editorActiveTabBackground: "#f9fafb", // Very light gray for active tab
+      editorActiveTabBorderColor: "#e5e7eb", // Match border color
+      editorTabBarBackground: "#ffffff",
+      editorTabBarBorderColor: "#e5e7eb",
+
+      // Terminal-style frame styling
+      terminalBackground: "#ffffff",
+      terminalTitlebarBackground: "#f9fafb",
+      terminalTitlebarForeground: "#6b7280", // Subtle gray text
+      terminalTitlebarBorderColor: "#e5e7eb",
+    },
+
+    // Focus and selection states
+    focusBorder: "var(--nextflow-green)", // Use site's green for focus
+    codeSelectionBackground: "var(--nextflow-light-green)", // Use site's light green
+
+    // Scrollbar styling
+    scrollbarThumbColor: "#d1d5db", // Light gray
+    scrollbarThumbHoverColor: "#9ca3af", // Slightly darker on hover
+
+    // Ensure clean, minimal appearance throughout
+    uiSelectionBackground: "var(--nextflow-light-green)",
+    uiSelectionForeground: "#1f2937", // Dark text for contrast
+
+    // Larger UI text for better readability of frame titles
+    uiFontSize: "1.2rem", // Increased from default 0.9rem for more prominent titles
+  },
+});

netlify.toml

@@ -23,20 +23,41 @@
 
 [[redirects]]
   from = "/example1.html"
-  to = "/basic-pipeline.html"
+  to = "/examples/basic-pipeline"
 
 [[redirects]]
   from = "/example2.html"
-  to = "/mixing-scripting-languages.html"
+  to = "/examples/mixing-scripting-languages"
 
 [[redirects]]
   from = "/example3.html"
-  to = "/blast-pipeline.html"
+  to = "/examples/blast-pipeline"
 
 [[redirects]]
   from = "/example4.html"
-  to = "/rna-seq-pipeline.html"
+  to = "/examples/rna-seq-pipeline"
 
 [[redirects]]
   from = "/example5.html"
-  to = "/machine-learning-pipeline.html"
+  to = "/examples/machine-learning-pipeline"
+
+# Direct redirects from old .html files to new structure
+[[redirects]]
+  from = "/basic-pipeline.html"
+  to = "/examples/basic-pipeline"
+
+[[redirects]]
+  from = "/mixing-scripting-languages.html"
+  to = "/examples/mixing-scripting-languages"
+
+[[redirects]]
+  from = "/blast-pipeline.html"
+  to = "/examples/blast-pipeline"
+
+[[redirects]]
+  from = "/rna-seq-pipeline.html"
+  to = "/examples/rna-seq-pipeline"
+
+[[redirects]]
+  from = "/machine-learning-pipeline.html"
+  to = "/examples/machine-learning-pipeline"