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feat: Reorganize pipeline examples into clean directory structure
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.
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‎netlify.toml‎

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

‎src/components/Footer.astro‎

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@@ -86,29 +86,30 @@ import LogoSeqera from "../../public/img/assets/Logo_Seqera_whote.svg";
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<ul class="examples-list pl-0">
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<li class="title text-white font-inter text-xs font-bold">Examples</li>
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<li>
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/basic-pipeline.html"
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/examples/basic-pipeline"
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>Basic pipeline</a
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>
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</li>
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<li>
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<a
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class="text-white font-inter text-xs font-normal leading-normal"
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href="/mixing-scripting-languages.html">Mixing scripting languages</a
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href="/examples/mixing-scripting-languages">Mixing scripting languages</a
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>
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</li>
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<li>
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/blast-pipeline.html"
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/examples/blast-pipeline"
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>BLAST pipeline</a
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>
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</li>
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<li>
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/rna-seq-pipeline.html"
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/examples/rna-seq-pipeline"
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>RNA-Seq pipeline</a
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>
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</li>
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<li>
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<a class="text-white font-inter text-xs font-normal leading-normal" href="/machine-learning-pipeline.html"
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>Machine Learning pipeline</a
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<a
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class="text-white font-inter text-xs font-normal leading-normal"
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href="/examples/machine-learning-pipeline">Machine Learning pipeline</a
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>
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</li>
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<li>

‎src/components/Menu/Menu.tsx‎

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@@ -192,27 +192,27 @@ const Menu = ({}) => {
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</a>
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<ul className="dropdown-menu" role="menu" onClick={handleMenuItemClick}>
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<li>
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<a href="/basic-pipeline.html" tabIndex={0}>
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<a href="/examples/basic-pipeline" tabIndex={0}>
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Basic pipeline
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</a>
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</li>
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<li>
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<a href="/mixing-scripting-languages.html" tabIndex={0}>
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<a href="/examples/mixing-scripting-languages" tabIndex={0}>
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Mixing scripting languages
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</a>
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</li>
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<li>
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<a href="/blast-pipeline.html" tabIndex={0}>
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<a href="/examples/blast-pipeline" tabIndex={0}>
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BLAST pipeline
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</a>
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</li>
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<li>
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<a href="/rna-seq-pipeline.html" tabIndex={0}>
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<a href="/examples/rna-seq-pipeline" tabIndex={0}>
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RNA-Seq pipeline
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</a>
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</li>
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<li>
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<a href="/machine-learning-pipeline.html" tabIndex={0}>
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<a href="/examples/machine-learning-pipeline" tabIndex={0}>
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Machine Learning pipeline
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</a>
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</li>

‎src/components/SideNavigation/ExamplesSideNav.tsx‎

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@@ -7,13 +7,11 @@ const ExamplesSideNav = () => {
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useEffect(() => {
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if (typeof window !== 'undefined') {
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const path = window.location.pathname;
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const filename = path.split('/').pop();
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if (filename) {
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const match = filename.match(/example(\d+)/);
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if (match && match[1]) {
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setActiveId(`example${match[1]}`);
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}
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// Extract pipeline name from /examples/pipeline-name/ format
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const match = path.match(/\/examples\/([^\/]+)\/?$/);
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if (match && match[1]) {
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setActiveId(match[1]);
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}
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}
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}, []);
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{
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id: 'basic-pipeline',
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title: 'Basic pipeline',
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href: 'basic-pipeline.html'
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href: '/examples/basic-pipeline'
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},
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{
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id: 'mixing-scripting-languages',
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title: 'Mixing scripting languages',
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href: 'mixing-scripting-languages.html'
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href: '/examples/mixing-scripting-languages'
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},
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{
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id: 'blast-pipeline',
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title: 'BLAST pipeline',
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href: 'blast-pipeline.html'
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href: '/examples/blast-pipeline'
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},
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{
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id: 'rna-seq-pipeline',
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title: 'RNA-Seq pipeline',
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href: 'rna-seq-pipeline.html'
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href: '/examples/rna-seq-pipeline'
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},
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{
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id: 'machine-learning-pipeline',
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title: 'Machine Learning pipeline',
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href: 'machine-learning-pipeline.html'
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href: '/examples/machine-learning-pipeline'
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}
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];
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‎src/pages/basic-pipeline.mdx‎ renamed to ‎src/pages/examples/basic-pipeline/index.mdx‎

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@@ -4,7 +4,7 @@ layout: "@layouts/ExampleLayout.astro"
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---
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import { Code } from "astro-expressive-code/components";
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import pipelineCode from "../examples/basic-pipeline.nf?raw";
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import pipelineCode from "./main.nf?raw";
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<div class="blg-summary example">
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<h2>Basic pipeline</h2>

‎src/examples/basic-pipeline.nf‎ renamed to ‎src/pages/examples/basic-pipeline/main.nf‎

File renamed without changes.

‎src/pages/examples/blast-pipeline/index.mdx‎

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---
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title: BLAST pipeline
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layout: "@layouts/ExampleLayout.astro"
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---
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import { Code } from "astro-expressive-code/components";
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import pipelineCode from "./main.nf?raw";
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<div class="blg-summary example">
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<h2>BLAST pipeline</h2>
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<p class="">
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This example splits a FASTA file into chunks and executes a BLAST query for each chunk in parallel. Then, all the
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sequences for the top hits are collected and merged into a single result file.
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</p>
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<Code code={pipelineCode} lang="nextflow" />
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</div>
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### Try it on your computer
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To run this pipeline on your computer, you will need:
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- Unix-like operating system
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- Java 17 (or higher)
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- Docker
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Install Nextflow by entering the following command in the terminal:
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$ curl -fsSL https://get.nextflow.io | bash
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Then launch the pipeline with this command:
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$ ./nextflow run blast-example -with-docker
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It will automatically download the pipeline [GitHub repository](https://github.com/nextflow-io/blast-example) and the associated Docker images, thus the first execution may take a few minutes to complete depending on your network connection.
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**NOTE**: To run this example with versions of Nextflow older than 22.04.0, you must include the `-dsl2` flag with `nextflow run`.

‎src/pages/blast-pipeline.md‎ renamed to ‎src/pages/examples/blast-pipeline/main.nf‎

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---
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title: BLAST pipeline
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layout: "@layouts/ExampleLayout.astro"
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---
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<div class="blg-summary example">
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<h2>BLAST pipeline</h2>
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<p class="">
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This example splits a FASTA file into chunks and executes a BLAST query for each chunk in parallel. Then, all the sequences for the top hits are collected and merged into a single result file.
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</p>
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```groovy
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#!/usr/bin/env nextflow
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/*
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"""
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blastdbcmd -db $db/$db_name -entry_batch top_hits | head -n 10 > sequences
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"""
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}
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```
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</div>
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### Try it on your computer
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To run this pipeline on your computer, you will need:
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- Unix-like operating system
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- Java 17 (or higher)
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- Docker
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Install Nextflow by entering the following command in the terminal:
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$ curl -fsSL https://get.nextflow.io | bash
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Then launch the pipeline with this command:
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$ ./nextflow run blast-example -with-docker
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It will automatically download the pipeline [GitHub repository](https://github.com/nextflow-io/blast-example) and the associated Docker images, thus the first execution may take a few minutes to complete depending on your network connection.
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**NOTE**: To run this example with versions of Nextflow older than 22.04.0, you must include the `-dsl2` flag with `nextflow run`.
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}

‎src/pages/examples.astro‎ renamed to ‎src/pages/examples/index.astro‎

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<p class="mb-4">
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Learn how to create a simple pipeline with two processes that communicate via channels.
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</p>
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<a href="basic-pipeline.html" class="text-nextflow-green hover:underline">View example →</a>
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<a href="/examples/basic-pipeline" class="text-nextflow-green hover:underline">View example →</a>
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</div>
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<div class="border rounded-lg p-6 hover:shadow-md transition-shadow">
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<h3 class="text-xl font-medium mb-2">Multiple inputs</h3>
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<p class="mb-4">
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Discover how to manage multiple inputs and complex data dependencies in your workflows.
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</p>
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<a href="mixing-scripting-languages.html" class="text-nextflow-green hover:underline">View example →</a>
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<a href="/examples/mixing-scripting-languages" class="text-nextflow-green hover:underline"
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>View example →</a
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>
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</div>
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<div class="border rounded-lg p-6 hover:shadow-md transition-shadow">
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<h3 class="text-xl font-medium mb-2">Channel operators</h3>
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<p class="mb-4">Explore powerful channel operators for transforming and manipulating data streams.</p>
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<a href="blast-pipeline.html" class="text-nextflow-green hover:underline">View example →</a>
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<a href="/examples/blast-pipeline" class="text-nextflow-green hover:underline">View example →</a>
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</div>
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<div class="border rounded-lg p-6 hover:shadow-md transition-shadow">
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<h3 class="text-xl font-medium mb-2">Processes and Channels</h3>
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<p class="mb-4">See advanced techniques for connecting processes through different channel types.</p>
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<a href="rna-seq-pipeline.html" class="text-nextflow-green hover:underline">View example →</a>
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<a href="/examples/rna-seq-pipeline" class="text-nextflow-green hover:underline">View example →</a>
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</div>
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<div class="border rounded-lg p-6 hover:shadow-md transition-shadow">
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<h3 class="text-xl font-medium mb-2">Error strategies</h3>
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<p class="mb-4">Learn how to handle errors and implement robust error recovery strategies.</p>
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<a href="machine-learning-pipeline.html" class="text-nextflow-green hover:underline">View example →</a>
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<a href="/examples/machine-learning-pipeline" class="text-nextflow-green hover:underline"
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>View example →</a
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>
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</div>
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</div>
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</div>

‎src/pages/examples/machine-learning-pipeline/index.mdx‎

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---
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title: Error strategies
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layout: "@layouts/ExampleLayout.astro"
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---
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import { Code } from "astro-expressive-code/components";
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import pipelineCode from "./main.nf?raw";
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<div class="blg-summary example">
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<h2>Machine Learning pipeline</h2>
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<p class="">
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This example shows how to put together a basic Machine Learning pipeline. It fetches a dataset from OpenML, trains a
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variety of machine learning models on a prediction target, and selects the best model based on some evaluation
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criteria.
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</p>
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<Code code={pipelineCode} lang="nextflow" />
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</div>
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### Try it in your computer
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To run this pipeline on your computer, you will need:
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- Unix-like operating system
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- Java 17 (or higher)
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- Docker
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Install Nextflow by entering the following command in the terminal:
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$ curl -fsSL get.nextflow.io | bash
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Then launch the pipeline with this command:
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$ nextflow run ml-hyperopt -profile wave
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It will automatically download the pipeline [GitHub repository](https://github.com/nextflow-io/ml-hyperopt) and build a Docker image on-the-fly using [Wave](https://seqera.io/wave/), thus the first execution may take a few minutes to complete depending on your network connection.
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**NOTE**: Nextflow 22.10.0 or newer is required to run this pipeline with Wave.

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