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molgenis · Dec 14, 2023 · d59ca5e · d59ca5e
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diff --git a/about/acknowledgements/index.html b/about/acknowledgements/index.html
@@ -146,6 +146,7 @@ <h1 id="acknowledgements">Acknowledgements<a class="headerlink" href="#acknowled
 <li><a href="https://github.com/tjiangHIT/cuteSV">cuteSV</a></li>
 <li><a href="https://github.com/philres/straglr">Straglr</a></li>
 <li><a href="https://github.com/Clinical-Genomics/stranger">Stranger</a></li>
+<li><a href="https://github.com/OpenGene/fastp">fastp</a></li>
 </ul>
 </div>
 </div><footer>

diff --git a/search/search_index.json b/search/search_index.json
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
diff --git a/usage/workflow/index.html b/usage/workflow/index.html
@@ -138,8 +138,9 @@ <h2 id="fastq">FASTQ<a class="headerlink" href="#fastq" title="Permanent link">
 <p>The <code>fastq</code> workflow consists of the following steps:</p>
 <ol>
 <li>Parallelize sample sheet per sample and for each sample</li>
-<li>In case of multiple fastq files per sample, concatenate the files</li>
+<li>Quality reporting and preprocessing using <a href="https://github.com/OpenGene/fastp">fastp</a></li>
 <li>Alignment using <a href="https://github.com/lh3/minimap2">minimap2</a> producing a <code>cram</code> file per sample</li>
+<li>In case of multiple fastq files per sample, concatenate the cram output files</li>
 <li>Continue with step 3. of the <code>cram</code> workflow</li>
 </ol>
 <p>For details, see <a href="https://github.com/molgenis/vip/blob/main/vip_fastq.nf">here</a>.</p>