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index.html

@@ -177,7 +177,7 @@ <h3 id="lateral-gene-transfer">Lateral gene transfer</h3>
 </ul>
 <h3 id="gene-order">Gene order</h3>
 <ul>
-<li>Comparison of genomic neighbourhoods using the Gene Order Workflow (<a href="https://github.com/JTL-lab/Gene-Order-Workflow"><code>Gene Order Workflow</code></a>) (in progress)</li>
+<li>Comparison of genomic neighbourhoods using the Gene Order Workflow (<a href="https://github.com/JTL-lab/Gene-Order-Workflow"><code>Gene Order Workflow</code></a>)</li>
 </ul>
 <p>See our <a href="ROADMAP/">roadmap</a> for a full list of future development targets.</p>
 <h2 id="quick-start">Quick Start <a name="quickstart"></a></h2>
@@ -351,5 +351,5 @@ <h2 id="citing-arete">Citing ARETE <a name="citing"></a></h2>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2023-11-07 13:48:56.739066+00:00
+Build Date UTC : 2023-11-12 14:15:03.420260+00:00
 -->

output/index.html

@@ -126,6 +126,8 @@
     </li>
         </ul>
     </li>
+    <li class="toctree-l2"><a class="reference internal" href="#gene-order">Gene Order</a>
+    </li>
     <li class="toctree-l2"><a class="reference internal" href="#pipeline-information">Pipeline information</a>
         <ul>
     <li class="toctree-l3"><a class="reference internal" href="#multiqc">MultiQC</a>
@@ -234,6 +236,9 @@ <h2 id="pipeline-overview">Pipeline overview</h2>
 </ul>
 </li>
 <li>
+<p><a href="#gene-order"><em>Gene Order</em></a></p>
+</li>
+<li>
 <p><a href="#phylogenomics-and-pangenomics">Phylogenomics and Pangenomics</a></p>
 <ul>
 <li><a href="#panaroo">Panaroo</a> or <a href="#ppanggolin"><em>PPanGGoLiN</em></a> - Pangenome alignment</li>
@@ -571,6 +576,18 @@ <h4 id="gubbins">Gubbins</h4>
 </li>
 </ul>
 <p><a href="https://github.com/nickjcroucher/gubbins">Gubbins</a> is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.</p>
+<h2 id="gene-order"><em>Gene Order</em></h2>
+<ul>
+<li>
+<p><code>gene-order/</code></p>
+<ul>
+<li><code>extraction/</code> - AMR genes of interest and their neighborhoods extracted from the assemblies.</li>
+<li><code>diamond/</code> - Pairwise alignments between all input genomes.</li>
+<li><code>clustering/</code> - Similarity and distance matrices for each AMR gene clustered via UPGMA, MCL and DBSCAN to identify similarities between their neighborhoods across all genomes.</li>
+</ul>
+</li>
+</ul>
+<p>Gene Order is a subworkflow for bacterial gene order analysis, with outputs easily explorable through its partner visualization application <a href="https://github.com/JTL-lab/Coeus">Coeus</a>.</p>
 <h2 id="pipeline-information">Pipeline information</h2>
 <ul>
 <li>

params/index.html

@@ -81,6 +81,8 @@
     </li>
     <li class="toctree-l2"><a class="reference internal" href="#poppunk">PopPUNK</a>
     </li>
+    <li class="toctree-l2"><a class="reference internal" href="#gene-order">Gene Order</a>
+    </li>
     <li class="toctree-l2"><a class="reference internal" href="#recombination">Recombination</a>
     </li>
     <li class="toctree-l2"><a class="reference internal" href="#dynamics">Dynamics</a>
@@ -142,7 +144,7 @@ <h2 id="inputoutput-options">Input/output options</h2>
 <td>Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.</small></details></td>
 <td><code>string</code></td>
 <td></td>
-<td>True</td>
+<td></td>
 <td></td>
 </tr>
 <tr>
@@ -444,7 +446,87 @@ <h2 id="poppunk">PopPUNK</h2>
 <td><code>accessory_similarity</code></td>
 <td>Similarity threshold for accessory genes</td>
 <td><code>number</code></td>
-<td>99</td>
+<td>99.0</td>
+<td></td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<h2 id="gene-order">Gene Order</h2>
+<p>Parameters for the Gene Order Subworkflow</p>
+<table>
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Description</th>
+<th>Type</th>
+<th>Default</th>
+<th>Required</th>
+<th>Hidden</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>run_gene_order</code></td>
+<td>Whether to run the Gene Order subworkflow</td>
+<td><code>boolean</code></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>gene_order_percent_cutoff</code></td>
+<td>Cutoff percentage of genomes a gene should be present within to be included in extraction and subsequent analysis. Should a float between 0 and 1 (e.g., 0.25 means only genes present in a minimum of 25% of genomes are kept).</td>
+<td><code>number</code></td>
+<td>0.25</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>gene_order_label_cols</code></td>
+<td>If using annotation files predicting features, list of space separated column names to be added to the gene names</td>
+<td><code>string</code></td>
+<td>None</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>num_neighbors</code></td>
+<td>Neighborhood size to extract. Should be an even number N, such that N/2 neighbors upstream and N/2 neighbors downstream will be analyzed.</td>
+<td><code>integer</code></td>
+<td>10</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>inflation</code></td>
+<td>Inflation hyperparameter value for Markov Clustering Algorithm.</td>
+<td><code>integer</code></td>
+<td>2</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>epsilon</code></td>
+<td>Epsilon hyperparameter value for DBSCAN clustering.</td>
+<td><code>number</code></td>
+<td>0.5</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>minpts</code></td>
+<td>Minpts hyperparameter value for DBSCAN clustering.</td>
+<td><code>integer</code></td>
+<td>5</td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>plot_clustering</code></td>
+<td>Create Clustering HTML Plots</td>
+<td><code>boolean</code></td>
+<td></td>
 <td></td>
 <td></td>
 </tr>