Deployed 7e494ab with MkDocs version: 1.5.3

index.html

@@ -351,5 +351,5 @@ <h2 id="citing-arete">Citing ARETE <a name="citing"></a></h2>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2023-10-16 12:16:12.428903+00:00
+Build Date UTC : 2023-10-23 23:02:15.603018+00:00
 -->

params/index.html

@@ -538,8 +538,8 @@ <h2 id="dynamics">Dynamics</h2>
 <tr>
 <td><code>max_support_threshold</code></td>
 <td>Maximum rSPR support threshold</td>
-<td><code>integer</code></td>
-<td>0</td>
+<td><code>number</code></td>
+<td>0.7</td>
 <td></td>
 <td></td>
 </tr>
@@ -551,6 +551,22 @@ <h2 id="dynamics">Dynamics</h2>
 <td></td>
 <td></td>
 </tr>
+<tr>
+<td><code>core_gene_tree</code></td>
+<td>Core (or reference) genome tree. Used in the rSPR entry.</td>
+<td><code>string</code></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+<tr>
+<td><code>concatenated_annotation</code></td>
+<td>TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE.</td>
+<td><code>string</code></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
 </tbody>
 </table>
 <h2 id="institutional-config-options">Institutional config options</h2>

usage/index.html

@@ -71,6 +71,8 @@
     <li class="toctree-l3"><a class="reference internal" href="#poppunk-entry">PopPUNK Entry</a>
     </li>
     <li class="toctree-l3"><a class="reference internal" href="#phylogenomics-and-pangenomics-entry">Phylogenomics and Pangenomics Entry</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#rspr-entry">rSPR Entry</a>
     </li>
         </ul>
     </li>
@@ -286,6 +288,27 @@ <h3 id="phylogenomics-and-pangenomics-entry">Phylogenomics and Pangenomics Entry
 <p>To execute phylogenomic and pangenomics analysis on pre-existing assemblies:</p>
 <pre><code class="language-bash">nextflow run beiko-lab/ARETE -entry phylogenomics --input_sample_table samplesheet.csv -profile docker
 </code></pre>
+<h3 id="rspr-entry">rSPR Entry</h3>
+<p>To execute the rSPR analysis on pre-existing trees:</p>
+<pre><code class="language-bash">nextflow run beiko-lab/ARETE \
+  -entry rspr \
+  --input_sample_table samplesheet.csv \
+  --core_gene_tree core_gene_alignment.tre \
+  --concatenated_annotation BAKTA.txt \
+  -profile docker
+</code></pre>
+<p>The parameters being:</p>
+<ul>
+<li><code>--core_gene_tree</code> - The reference tree, coming from a core genome alignment, like the one generated by panaroo in ARETE.</li>
+<li><code>--concatenated_annotation</code> - The tabular annotation results (TSV) for all genomes, like the ones generated at the end of Prokka or Bakta in ARETE. Although useful, it's not necessary to execute the rSPR entry.</li>
+<li><code>--input_sample_table</code> - A samplesheet containing all individual gene trees in the following format:</li>
+</ul>
+<p><code>gene_tree,path
+CDS_0000,/path/to/CDS_0000.tre
+CDS_0001,/path/to/CDS_0001.tre
+CDS_0002,/path/to/CDS_0002.tre
+CDS_0003,/path/to/CDS_0003.tre
+CDS_0004,/path/to/CDS_0004.tre</code></p>
 <h2 id="updating-the-pipeline">Updating the pipeline</h2>
 <p>When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:</p>
 <pre><code class="language-bash">nextflow pull beiko-lab/ARETE