feat: Reorganize pipeline examples into clean directory structure #424
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- 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.
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- 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 <[email protected]>
Restructure pipeline examples from flat files to organized subdirectories under /examples/, with colocated docs and code files. - Move examples.astro → examples/index.astro - Create subdirs: basic-pipeline/, blast-pipeline/, rna-seq-pipeline/, machine-learning-pipeline/, mixing-scripting-languages/ - Extract embedded Nextflow code from .md to separate main.nf files - Convert .md to .mdx with Expressive Code imports - Clean URLs without trailing slashes (/examples/basic-pipeline) - Update all navigation and links to new structure - Fix active page highlighting in side navigation - Add backward compatibility redirects Better organization, consistent patterns, maintainable structure.
Rename all main.nf files to _main.nf and update corresponding import statements to prevent Astro from treating pipeline files as pages. - Rename: main.nf → _main.nf in all pipeline subdirectories - Update imports: './main.nf?raw' → './_main.nf?raw' in all .mdx files - Eliminates console warnings about unsupported file types - Maintains functionality while following Astro conventions
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Summary
Restructure pipeline examples from flat files to organized subdirectories under
/examples/, with colocated docs and code files.Changes
Dependencies
Better organization, consistent patterns, maintainable structure.