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docs/getting-started/index.html

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 <h1 id="getting-started">Getting started</h1>
-<p>This guide helps you to understand the concepts of nf-test and to write your first test cases. Before you start, please check if you have <a href="/docs/installation.md">installed</a> nf-test properly on your computer. Also, this guide assumes that you have a basic knowledge of Groovy and unit testing. The <a href="http://groovy-lang.org/documentation.html">Groovy documentation</a> is the best place to learn its syntax.</p>
+<p>This guide helps you to understand the concepts of nf-test and to write your first test cases. Before you start, please check if you have <a href="../../installation/">installed</a> nf-test properly on your computer. Also, this guide assumes that you have a basic knowledge of Groovy and unit testing. The <a href="http://groovy-lang.org/documentation.html">Groovy documentation</a> is the best place to learn its syntax.</p>
 <h2 id="lets-get-started">Let's get started</h2>
 <p>To show the power of nf-test, we adapted a recently published <a href="https://github.com/GoekeLab/bioinformatics-workflows/tree/master/nextflow">proof of concept Nextflow pipeline</a>. We adapted the pipeline to the new DSL2 syntax using modules. First, open the terminal and clone our test pipeline:</p>
 <div class="highlight"><pre><span></span><code><span class="c1"># clone nextflow pipeline</span>

index.html

@@ -1338,15 +1338,15 @@ <h2 id="unit-testing"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/s
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-<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> Learn more about <a href="docs/testcases/nextflow_pipeline">pipeline tests</a>, <a href="docs/testcases/nextflow_workflow">workflow tests</a>, <a href="docs/testcases/nextflow_process">process tests</a> and <a href="docs/testcases/nextflow_function">function tests</a> in the documentation.</p>
+<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> Learn more about <a href="docs/testcases/nextflow_pipeline/">pipeline tests</a>, <a href="docs/testcases/nextflow_workflow/">workflow tests</a>, <a href="docs/testcases/nextflow_process/">process tests</a> and <a href="docs/testcases/nextflow_function/">function tests</a> in the documentation.</p>
 <hr />
 <h2 id="snapshot-testing"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 3H5c-1.1 0-2 .9-2 2v14a2 2 0 0 0 2 2h6.81c-.39-.66-.64-1.4-.74-2.16a2.994 2.994 0 0 1-1.87-3.81C9.61 13.83 10.73 13 12 13c.44 0 .88.1 1.28.29 2.29-1.79 5.55-1.7 7.72.25V7l-4-4m-2 6H5V5h10v4m.75 12L13 18l1.16-1.16 1.59 1.59 3.59-3.59 1.16 1.41L15.75 21"/></svg></span> Snapshot testing</h2>
 <p>nf-test supports <strong>snapshot testing</strong> and automatically <strong>generates a baseline set of unit tests</strong> to safeguard against regressions caused by changes.</br>nf-test captures a snapshot of output channels or any other objects and subsequently compares them to reference snapshot files stored alongside the tests. If the two snapshots do not match, the test will fail</p>
-<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> <a href="docs/assertions/snapshots">Learn more</a></p>
+<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> <a href="docs/assertions/snapshots/">Learn more</a></p>
 <hr />
 <h2 id="highly-extendable"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M16 7V3h-2v4h-4V3H8v4C7 7 6 8 6 9v5.5L9.5 18v3h5v-3l3.5-3.5V9c0-1-1-2-2-2m0 6.67-2.91 2.92-.42.41h-1.34l-.41-.41L8 13.67V9.09c0-.03.06-.09.09-.09h7.83c.03 0 .08.06.08.09v4.58Z"/></svg></span> Highly extendable</h2>
-<p>nf-test supports the <strong>inclusion of third-party libraries</strong> (e.g., jar files) or functions from Groovy files. This can be done to either extend its functionality or to prevent code duplication, thus maintaining simplicity in the logic of test cases. Given that many assertions are specific to use cases, nf-test incorporates a <strong>plugin system</strong> that allows for the extension of existing classes with custom methods. For example <a href="docs/assertions/fasta">FASTA file support</a>.</p>
-<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> <a href="docs/assertions/libraries">Learn more</a></p>
+<p>nf-test supports the <strong>inclusion of third-party libraries</strong> (e.g., jar files) or functions from Groovy files. This can be done to either extend its functionality or to prevent code duplication, thus maintaining simplicity in the logic of test cases. Given that many assertions are specific to use cases, nf-test incorporates a <strong>plugin system</strong> that allows for the extension of existing classes with custom methods. For example <a href="docs/assertions/fasta/">FASTA file support</a>.</p>
+<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg></span> <a href="docs/assertions/libraries/">Learn more</a></p>
 <hr />
 <h2 id="support-us"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 17.27 18.18 21l-1.64-7.03L22 9.24l-7.19-.62L12 2 9.19 8.62 2 9.24l5.45 4.73L5.82 21 12 17.27Z"/></svg></span> Support us</h2>
 <p>We love stars as much as we love rockets! So make sure you <a href="https://github.com/askimed/nf-test">star us on GitHub</a>.</p>

installation/index.html

@@ -1272,7 +1272,7 @@ <h3 id="verify-installation">Verify installation</h3>
       cite doi:10.1038/nbt.3820
       http://nextflow.io
 </code></pre></div>
-<p>Now you are ready to write your <a href="getting-started.md">first testcase</a>.</p>
+<p>Now you are ready to write your <a href="../docs/getting-started/">first testcase</a>.</p>
 <h3 id="install-a-specific-version">Install a specific version</h3>
 <p>If you want to install a specific version pass it to the install script as so</p>
 <div class="highlight"><pre><span></span><code>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://code.askimed.com/install/nf-test<span class="w"> </span><span class="p">|</span><span class="w"> </span>bash<span class="w"> </span>-s<span class="w"> </span><span class="m">0</span>.7.0