From f2c897a83fd8f2bfebd3aa5524570d43eb779b9a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 19 Sep 2025 22:07:13 -0500 Subject: [PATCH 1/2] feat: Integrate Expressive Code with site design - Configure comprehensive style overrides to match site's clean, minimal aesthetic - Use pure white backgrounds and site's CSS variables (--nextflow-green colors) - Set proper text marker highlighting with site's light green accent color - Remove frame titles and switch to 'nextflow' language for syntax highlighting - Maintain advanced highlighting functionality while achieving visual integration - Result: Code blocks now blend seamlessly with site design while providing enhanced educational features The example pages now have clean, professional code blocks that match the site's design system perfectly, with clearly visible line highlighting using the site's signature green color scheme. --- astro.config.mjs | 73 ++++++++- package-lock.json | 313 +++++++++++++++++++++++++++++++++++- package.json | 1 + src/pages/basic-pipeline.md | 2 +- 4 files changed, 378 insertions(+), 11 deletions(-) diff --git a/astro.config.mjs b/astro.config.mjs index 22355017e..d2c0ba2d6 100644 --- a/astro.config.mjs +++ b/astro.config.mjs @@ -3,7 +3,7 @@ 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 react from "@astrojs/react"; import tailwind from "@astrojs/tailwind"; @@ -12,12 +12,6 @@ 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 +46,71 @@ export default defineConfig({ ], }, integrations: [ + expressiveCode({ + // Use light theme for consistency with site design + themes: ["github-light"], + // Enable advanced features + plugins: ["text-markers", "frames"], + // 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: "0.875rem", // 14px - readable code size + 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 + }, + + // 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 + }, + }), react(), tailwind(), sitemap({ diff --git a/package-lock.json b/package-lock.json index 70340d994..86467d0cf 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,6 +14,7 @@ "@astrojs/sitemap": "^3.1.6", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", + "astro-expressive-code": "^0.41.3", "astro-remark-description": "^1.1.2", "react": "^19.0.0", "react-cookie": 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"dependencies": { + "@types/hast": "^3.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/hast-util-to-text": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/hast-util-to-text/-/hast-util-to-text-4.0.2.tgz", @@ -5408,6 +5691,18 @@ "node": ">=0.10.0" } }, + "node_modules/nth-check": { + "version": "2.1.1", + "resolved": "https://registry.npmjs.org/nth-check/-/nth-check-2.1.1.tgz", + "integrity": "sha512-lqjrjmaOoAnWfMmBPL+XNnynZh2+swxiX3WUE0s4yEHI6m+AwrK2UZOimIRl3X/4QctVqS8AiZjFqyOGrMXb/w==", + "license": "BSD-2-Clause", + "dependencies": { + "boolbase": "^1.0.0" + }, + "funding": { + "url": "https://github.com/fb55/nth-check?sponsor=1" + } + }, "node_modules/object-assign": { "version": "4.1.1", "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz", @@ -5443,6 +5738,12 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/oniguruma-parser": { + "version": "0.12.1", + "resolved": "https://registry.npmjs.org/oniguruma-parser/-/oniguruma-parser-0.12.1.tgz", + "integrity": "sha512-8Unqkvk1RYc6yq2WBYRj4hdnsAxVze8i7iPfQr8e4uSP3tRv0rpZcbGUDvxfQQcdwHt/e9PrMvGCsa8OqG9X3w==", + "license": "MIT" + }, "node_modules/oniguruma-to-es": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/oniguruma-to-es/-/oniguruma-to-es-2.3.0.tgz", @@ -5830,7 +6131,6 @@ "version": "6.2.0", "resolved": "https://registry.npmjs.org/postcss-nested/-/postcss-nested-6.2.0.tgz", "integrity": "sha512-HQbt28KulC5AJzG+cZtj9kvKB93CFCdLvog1WFLf1D+xmMvPGlBstkpTEZfK5+AN9hfJocyBFCNiqyS48bpgzQ==", - "dev": true, "funding": [ { "type": "opencollective", @@ -5856,7 +6156,6 @@ "version": "6.1.2", "resolved": "https://registry.npmjs.org/postcss-selector-parser/-/postcss-selector-parser-6.1.2.tgz", "integrity": "sha512-Q8qQfPiZ+THO/3ZrOrO0cJJKfpYCagtMUkXbnEfmgUjwXg6z/WBeOyS9APBBPCTSiDV+s4SwQGu8yFsiMRIudg==", - "dev": true, "license": "MIT", "dependencies": { "cssesc": "^3.0.0", @@ -6093,6 +6392,15 @@ "url": "https://opencollective.com/unified" } }, + "node_modules/rehype-expressive-code": { + "version": "0.41.3", + "resolved": "https://registry.npmjs.org/rehype-expressive-code/-/rehype-expressive-code-0.41.3.tgz", + "integrity": "sha512-8d9Py4c/V6I/Od2VIXFAdpiO2kc0SV2qTJsRAaqSIcM9aruW4ASLNe2kOEo1inXAAkIhpFzAHTc358HKbvpNUg==", + "license": "MIT", + "dependencies": { + "expressive-code": "^0.41.3" + } + }, "node_modules/rehype-parse": { "version": "9.0.1", "resolved": "https://registry.npmjs.org/rehype-parse/-/rehype-parse-9.0.1.tgz", @@ -7319,7 +7627,6 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz", "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==", - "dev": true, "license": "MIT" }, "node_modules/vfile": { diff --git a/package.json b/package.json index dd21a83a0..197b13fcc 100644 --- a/package.json +++ b/package.json @@ -17,6 +17,7 @@ "@astrojs/sitemap": "^3.1.6", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", + "astro-expressive-code": "^0.41.3", "astro-remark-description": "^1.1.2", "react": "^19.0.0", "react-cookie": "^7.2.2", diff --git a/src/pages/basic-pipeline.md b/src/pages/basic-pipeline.md index 074e9bc7a..cb3ee61ee 100644 --- a/src/pages/basic-pipeline.md +++ b/src/pages/basic-pipeline.md @@ -10,7 +10,7 @@ layout: "@layouts/ExampleLayout.astro" This example shows how to write a pipeline with two simple Bash processes, so that the results produced by the first process are consumed by the second process.

-```groovy +```nextflow {1,3,8-18,21-32,39-43} #!/usr/bin/env nextflow params.in = "$baseDir/data/sample.fa" From b40db46371b7779f8d3ab776461656b6f3b3b873 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sat, 20 Sep 2025 14:04:12 +0300 Subject: [PATCH 2/2] feat: implement Expressive Code with line numbers and improved styling MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Create separate ec.config.mjs for Expressive Code plugin configuration - Install @expressive-code/plugin-line-numbers plugin - Enable line numbers by default with showLineNumbers: true - Set optimal font size (1.5rem/24px) for better code readability - Simplify astro.config.mjs to use basic expressiveCode() integration - Maintain all existing styling and text marker functionality - Fix MDX Code component compatibility with plugin-based configuration - Support external file imports with ?raw suffix for clean separation 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- astro.config.mjs | 69 +- ec.config.mjs | 76 ++ package-lock.json | 673 ++++++++++++++++++ package.json | 2 + src/examples/basic-pipeline.nf | 44 ++ src/layouts/ExampleLayout.astro | 2 - .../{basic-pipeline.md => basic-pipeline.mdx} | 55 +- 7 files changed, 806 insertions(+), 115 deletions(-) create mode 100644 ec.config.mjs create mode 100644 src/examples/basic-pipeline.nf rename src/pages/{basic-pipeline.md => basic-pipeline.mdx} (74%) diff --git a/astro.config.mjs b/astro.config.mjs index d2c0ba2d6..5671a456a 100644 --- a/astro.config.mjs +++ b/astro.config.mjs @@ -4,6 +4,8 @@ import remarkDescription from "astro-remark-description"; import remarkDirective from "remark-directive"; import sitemap from "@astrojs/sitemap"; 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"; @@ -46,71 +48,8 @@ export default defineConfig({ ], }, integrations: [ - expressiveCode({ - // Use light theme for consistency with site design - themes: ["github-light"], - // Enable advanced features - plugins: ["text-markers", "frames"], - // 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: "0.875rem", // 14px - readable code size - 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 - }, - - // 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 - }, - }), + expressiveCode(), + mdx(), react(), tailwind(), sitemap({ diff --git a/ec.config.mjs b/ec.config.mjs new file mode 100644 index 000000000..5c8d704b7 --- /dev/null +++ b/ec.config.mjs @@ -0,0 +1,76 @@ +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: "1.5rem", // 24px - much larger, very readable code size + 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 + }, + + // 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 + }, +}); diff --git a/package-lock.json b/package-lock.json index 86467d0cf..2bb248b78 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,9 +9,11 @@ "version": "0.0.1", "dependencies": { "@astrojs/check": "^0.9.3", + "@astrojs/mdx": "^3.1.9", "@astrojs/react": "^4.2.1", "@astrojs/rss": "^4.0.7", "@astrojs/sitemap": "^3.1.6", + "@expressive-code/plugin-line-numbers": "^0.41.3", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", "astro-expressive-code": "^0.41.3", @@ -154,6 +156,34 @@ "vfile": "^6.0.3" } }, + "node_modules/@astrojs/mdx": { + "version": "3.1.9", + "resolved": "https://registry.npmjs.org/@astrojs/mdx/-/mdx-3.1.9.tgz", + "integrity": "sha512-3jPD4Bff6lIA20RQoonnZkRtZ9T3i0HFm6fcDF7BMsKIZ+xBP2KXzQWiuGu62lrVCmU612N+SQVGl5e0fI+zWg==", + "license": "MIT", + "dependencies": { + "@astrojs/markdown-remark": "5.3.0", + "@mdx-js/mdx": "^3.1.0", + "acorn": "^8.14.0", + "es-module-lexer": "^1.5.4", + "estree-util-visit": "^2.0.0", + "gray-matter": "^4.0.3", + "hast-util-to-html": "^9.0.3", + "kleur": "^4.1.5", + "rehype-raw": "^7.0.0", + "remark-gfm": "^4.0.0", + "remark-smartypants": "^3.0.2", + "source-map": "^0.7.4", + "unist-util-visit": "^5.0.0", + "vfile": "^6.0.3" + }, + "engines": { + "node": "^18.17.1 || ^20.3.0 || >=21.0.0" + }, + "peerDependencies": { + "astro": "^4.8.0" + } + }, "node_modules/@astrojs/prism": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/@astrojs/prism/-/prism-3.1.0.tgz", @@ -1050,6 +1080,15 @@ "@expressive-code/core": "^0.41.3" } }, + "node_modules/@expressive-code/plugin-line-numbers": { + "version": "0.41.3", + "resolved": "https://registry.npmjs.org/@expressive-code/plugin-line-numbers/-/plugin-line-numbers-0.41.3.tgz", + "integrity": "sha512-eig82a4CRC3XgVPQ2S/TMDcLiHJokOCD/mAdNVImpD3segVewxfjGgtj5DXQRo0E0q6f0R0EH34YzTFl5CEPqg==", + "license": "MIT", + "dependencies": { + "@expressive-code/core": "^0.41.3" + } + }, "node_modules/@expressive-code/plugin-shiki": { "version": "0.41.3", "resolved": "https://registry.npmjs.org/@expressive-code/plugin-shiki/-/plugin-shiki-0.41.3.tgz", @@ -1645,6 +1684,43 @@ "@jridgewell/sourcemap-codec": "^1.4.14" } }, + "node_modules/@mdx-js/mdx": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/@mdx-js/mdx/-/mdx-3.1.1.tgz", + "integrity": "sha512-f6ZO2ifpwAQIpzGWaBQT2TXxPv6z3RBzQKpVftEWN78Vl/YweF1uwussDx8ECAXVtr3Rs89fKyG9YlzUs9DyGQ==", + "license": "MIT", + "dependencies": { + "@types/estree": "^1.0.0", + "@types/estree-jsx": "^1.0.0", + "@types/hast": "^3.0.0", + "@types/mdx": "^2.0.0", + "acorn": "^8.0.0", + "collapse-white-space": "^2.0.0", + "devlop": "^1.0.0", + "estree-util-is-identifier-name": "^3.0.0", + "estree-util-scope": "^1.0.0", + "estree-walker": "^3.0.0", + "hast-util-to-jsx-runtime": "^2.0.0", + "markdown-extensions": "^2.0.0", + "recma-build-jsx": "^1.0.0", + "recma-jsx": "^1.0.0", + "recma-stringify": "^1.0.0", + "rehype-recma": "^1.0.0", + "remark-mdx": "^3.0.0", + "remark-parse": "^11.0.0", + "remark-rehype": "^11.0.0", + "source-map": "^0.7.0", + "unified": "^11.0.0", + "unist-util-position-from-estree": "^2.0.0", + "unist-util-stringify-position": "^4.0.0", + "unist-util-visit": "^5.0.0", + "vfile": "^6.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/@nodelib/fs.scandir": { "version": "2.1.5", "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz", @@ -2113,6 +2189,15 @@ "integrity": 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"hast-util-to-estree": "^3.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/rehype-stringify": { "version": "10.0.1", "resolved": "https://registry.npmjs.org/rehype-stringify/-/rehype-stringify-10.0.1.tgz", @@ -6480,6 +7099,20 @@ "url": "https://opencollective.com/unified" } }, + "node_modules/remark-mdx": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/remark-mdx/-/remark-mdx-3.1.1.tgz", + "integrity": "sha512-Pjj2IYlUY3+D8x00UJsIOg5BEvfMyeI+2uLPn9VO9Wg4MEtN/VTIq2NEJQfde9PnX15KgtHyl9S0BcTnWrIuWg==", + "license": "MIT", + "dependencies": { + "mdast-util-mdx": "^3.0.0", + "micromark-extension-mdxjs": "^3.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/remark-parse": { "version": "11.0.0", "resolved": "https://registry.npmjs.org/remark-parse/-/remark-parse-11.0.0.tgz", @@ -6932,6 +7565,15 @@ "integrity": 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+ "resolved": "https://registry.npmjs.org/style-to-object/-/style-to-object-1.0.9.tgz", + "integrity": "sha512-G4qppLgKu/k6FwRpHiGiKPaPTFcG3g4wNVX/Qsfu+RqQM30E7Tyu/TEgxcL9PNLF5pdRLwQdE3YKKf+KF2Dzlw==", + "license": "MIT", + "dependencies": { + "inline-style-parser": "0.2.4" + } + }, "node_modules/sucrase": { "version": "3.35.0", "resolved": "https://registry.npmjs.org/sucrase/-/sucrase-3.35.0.tgz", @@ -7514,6 +8174,19 @@ "url": "https://opencollective.com/unified" } }, + "node_modules/unist-util-position-from-estree": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/unist-util-position-from-estree/-/unist-util-position-from-estree-2.0.0.tgz", + "integrity": "sha512-KaFVRjoqLyF6YXCbVLNad/eS4+OfPQQn2yOd7zF/h5T/CSL2v8NpN6a5TPvtbXthAGw5nG+PuTtq+DdIZr+cRQ==", + "license": "MIT", + "dependencies": { + "@types/unist": "^3.0.0" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/unified" + } + }, "node_modules/unist-util-remove-position": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/unist-util-remove-position/-/unist-util-remove-position-5.0.0.tgz", diff --git a/package.json b/package.json index 197b13fcc..51cada0c7 100644 --- a/package.json +++ b/package.json @@ -12,9 +12,11 @@ }, "dependencies": { "@astrojs/check": "^0.9.3", + "@astrojs/mdx": "^3.1.9", "@astrojs/react": "^4.2.1", "@astrojs/rss": "^4.0.7", "@astrojs/sitemap": "^3.1.6", + "@expressive-code/plugin-line-numbers": "^0.41.3", "@shikijs/transformers": "^1.6.3", "astro": "^4.16.1", "astro-expressive-code": "^0.41.3", diff --git a/src/examples/basic-pipeline.nf b/src/examples/basic-pipeline.nf new file mode 100644 index 000000000..2fa01043f --- /dev/null +++ b/src/examples/basic-pipeline.nf @@ -0,0 +1,44 @@ +#!/usr/bin/env nextflow + +params.in = "$baseDir/data/sample.fa" + +/* + * Split a fasta file into multiple files + */ +process splitSequences { + + input: + path 'input.fa' + + output: + path 'seq_*' + + """ + awk '/^>/{f="seq_"++d} {print > f}' < input.fa + """ +} + +/* + * Reverse the sequences + */ +process reverse { + + input: + path x + + output: + stdout + + """ + cat $x | rev + """ +} + +/* + * Define the workflow + */ +workflow { + splitSequences(params.in) \ + | reverse \ + | view +} \ No newline at end of file diff --git a/src/layouts/ExampleLayout.astro b/src/layouts/ExampleLayout.astro index b99775ac4..f69745552 100644 --- a/src/layouts/ExampleLayout.astro +++ b/src/layouts/ExampleLayout.astro @@ -1,7 +1,6 @@ --- import Page from "./Page.astro"; import ExamplesSideNav from "@components/SideNavigation/ExamplesSideNav"; -import CodeCopyButton from "@components/CodeBlock/CodeCopy"; import "../components/CodeBlock/styles.css"; const { frontmatter } = Astro.props; @@ -21,7 +20,6 @@ const image = frontmatter?.image || "";
- diff --git a/src/pages/basic-pipeline.md b/src/pages/basic-pipeline.mdx similarity index 74% rename from src/pages/basic-pipeline.md rename to src/pages/basic-pipeline.mdx index cb3ee61ee..136be2c75 100644 --- a/src/pages/basic-pipeline.md +++ b/src/pages/basic-pipeline.mdx @@ -3,59 +3,18 @@ title: Basic pipeline layout: "@layouts/ExampleLayout.astro" --- +import { Code } from "astro-expressive-code/components"; +import pipelineCode from "../examples/basic-pipeline.nf?raw"; +

Basic pipeline

-

- This example shows how to write a pipeline with two simple Bash processes, so that the results produced by the first process are consumed by the second process. +

+ This example shows how to write a pipeline with two simple Bash processes, so that the results produced by the first + process are consumed by the second process.

-```nextflow {1,3,8-18,21-32,39-43} -#!/usr/bin/env nextflow - -params.in = "$baseDir/data/sample.fa" - -/* - * Split a fasta file into multiple files - */ -process splitSequences { - - input: - path 'input.fa' - - output: - path 'seq_*' - - """ - awk '/^>/{f="seq_"++d} {print > f}' < input.fa - """ -} - -/* - * Reverse the sequences - */ -process reverse { - - input: - path x - - output: - stdout - - """ - cat $x | rev - """ -} - -/* - * Define the workflow - */ -workflow { - splitSequences(params.in) \ - | reverse \ - | view -} -``` +