version++ to v1.3.13; render docs

BioLockJ-Dev-Team · Nov 10, 2020 · 7cd4857 · 7cd4857
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diff --git a/.version b/.version
@@ -1 +1 @@
-v1.3.12
+v1.3.13
diff --git a/docs/GENERATED/BioLockJ-Api/index.html b/docs/GENERATED/BioLockJ-Api/index.html
@@ -219,7 +219,7 @@ <h1 id="biolockj-api">BioLockJ API<a class="headerlink" href="#biolockj-api" tit
 <p>BioLockJ comes with an API.                                      </p>
 <p>For the most up-to-date information about how to use the API, see the help menu:                                      </p>
 <p><code>biolockj-api help</code>                   </p>
-<pre><code>BioLockJ API v1.3.12 - UNCC Fodor Lab                   
+<pre><code>BioLockJ API v1.3.13 - UNCC Fodor Lab                   
 
 Usage:                   
 (bash)                   

diff --git a/docs/GENERATED/General-Properties/index.html b/docs/GENERATED/General-Properties/index.html
@@ -440,6 +440,10 @@ <h3 id="input"><a href="../Input/">input</a><a class="headerlink" href="#input"
 </thead>
 <tbody>
 <tr>
+<td align="left"><em>input.allowDuplicateNames</em></td>
+<td align="left"><em>boolean</em> <br>Should files with the same name be permitted in inputs. File names are used to link data to metadata, and duplicated names create ambiguity.  However in some pipelines, duplicates are appropriate.<br><em>default:</em>  N</td>
+</tr>
+<tr>
 <td align="left"><em>input.dirPaths</em></td>
 <td align="left"><em>list of file paths</em> <br>List of one or more directories containing the pipeline input data.<br><em>default:</em>  <em>null</em></td>
 </tr>

diff --git a/docs/GENERATED/Input/index.html b/docs/GENERATED/Input/index.html
@@ -236,6 +236,10 @@ <h1 id="input">Input<a class="headerlink" href="#input" title="Permanent link">#
 </thead>
 <tbody>
 <tr>
+<td align="left"><em>input.allowDuplicateNames</em></td>
+<td align="left"><em>boolean</em> <br>Should files with the same name be permitted in inputs. File names are used to link data to metadata, and duplicated names create ambiguity.  However in some pipelines, duplicates are appropriate.<br><em>default:</em>  N</td>
+</tr>
+<tr>
 <td align="left"><em>input.dirPaths</em></td>
 <td align="left"><em>list of file paths</em> <br>List of one or more directories containing the pipeline input data.<br><em>default:</em>  <em>null</em></td>
 </tr>

diff --git a/docs/GENERATED/biolockj-help/index.html b/docs/GENERATED/biolockj-help/index.html
@@ -217,7 +217,7 @@
 </code></pre>
 
 <pre><code class="bash">
-BioLockJ v1.3.12 - UNCC Fodor Lab July 2018                   
+BioLockJ v1.3.13 - UNCC Fodor Lab July 2018                   
 Usage:                   
   biolockj [options] &lt;config|pipeline&gt;                   
 

diff --git a/docs/GENERATED/biolockj.module.assembly/GenomeAssembly/index.html b/docs/GENERATED/biolockj.module.assembly/GenomeAssembly/index.html
@@ -305,7 +305,7 @@ <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanen
 PRODIGAL                 <br />
 https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux                   </p>
 <p>Module developed by Shan Sun                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.classifier.r16s/RdpClassifier/index.html b/docs/GENERATED/biolockj.module.classifier.r16s/RdpClassifier/index.html
@@ -315,7 +315,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 biolockj.module.implicit.parser.r16s.RdpParser                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/rdp_classifier:v1.3.12
+<pre><code>biolockjdevteam/rdp_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -324,7 +324,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>RdpClassifier.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.classifier.wgs/Humann2Classifier/index.html b/docs/GENERATED/biolockj.module.classifier.wgs/Humann2Classifier/index.html
@@ -315,7 +315,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 biolockj.module.implicit.parser.wgs.Humann2Parser                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/humann2_classifier:v1.3.12
+<pre><code>biolockjdevteam/humann2_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.classifier.wgs/Kraken2Classifier/index.html b/docs/GENERATED/biolockj.module.classifier.wgs/Kraken2Classifier/index.html
@@ -303,7 +303,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 biolockj.module.implicit.parser.wgs.Kraken2Parser                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/kraken2_classifier:v1.3.12
+<pre><code>biolockjdevteam/kraken2_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.classifier.wgs/KrakenClassifier/index.html b/docs/GENERATED/biolockj.module.classifier.wgs/KrakenClassifier/index.html
@@ -304,7 +304,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 biolockj.module.implicit.parser.wgs.KrakenParser                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/kraken_classifier:v1.3.12
+<pre><code>biolockjdevteam/kraken_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.classifier.wgs/Metaphlan2Classifier/index.html b/docs/GENERATED/biolockj.module.classifier.wgs/Metaphlan2Classifier/index.html
@@ -307,7 +307,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 biolockj.module.implicit.parser.wgs.Metaphlan2Parser                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/metaphlan2_classifier:v1.3.12
+<pre><code>biolockjdevteam/metaphlan2_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.diversity/ShannonDiversity/index.html b/docs/GENERATED/biolockj.module.diversity/ShannonDiversity/index.html
@@ -282,7 +282,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -291,7 +291,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>ShannonDiversity.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Anthony Fodor                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.diy/GenMod/index.html b/docs/GENERATED/biolockj.module.diy/GenMod/index.html
@@ -333,15 +333,15 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/blj_basic:v1.3.12
+<pre><code>biolockjdevteam/blj_basic:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
 <code>GenMod.imageOwner</code><br>
 <code>GenMod.imageName</code><br>
 <code>GenMod.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
-<p>BioLockJ v1.3.12</p>
+<p>BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.diy/Rmarkdown/index.html b/docs/GENERATED/biolockj.module.diy/Rmarkdown/index.html
@@ -312,7 +312,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>Rmarkdown.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module created by Ivory Blakley                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.getData.sra/SraDownload/index.html b/docs/GENERATED/biolockj.module.getData.sra/SraDownload/index.html
@@ -322,7 +322,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/sratoolkit:v1.3.12
+<pre><code>biolockjdevteam/sratoolkit:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -332,7 +332,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p><a href="https://github.com/ncbi/sra-tools">sra-tools</a>                 <br />
 Module developed by Philip Badzuh                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.getData.sra/SraMetaDB/index.html b/docs/GENERATED/biolockj.module.getData.sra/SraMetaDB/index.html
@@ -311,7 +311,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/blj_basic:v1.3.12
+<pre><code>biolockjdevteam/blj_basic:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -320,7 +320,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>SraMetaDB.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Malcolm Zapatas and Ivory Blakley                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.getData.sra/SraMetaData/index.html b/docs/GENERATED/biolockj.module.getData.sra/SraMetaData/index.html
@@ -303,7 +303,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/pysradb:v1.3.12
+<pre><code>biolockjdevteam/pysradb:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -312,7 +312,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>SraMetaData.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Malcolm Zapatas and Ivory Blakley                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.getData.sra/SrpSrrConverter/index.html b/docs/GENERATED/biolockj.module.getData.sra/SrpSrrConverter/index.html
@@ -317,7 +317,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>SrpSrrConverter.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Malcolm Zapatas and Ivory Blakley                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.r16s/QiimeParser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.r16s/QiimeParser/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.r16s/RdpParser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.r16s/RdpParser/index.html
@@ -303,7 +303,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -312,7 +312,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>RdpParser.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.wgs/Humann2Parser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.wgs/Humann2Parser/index.html
@@ -307,7 +307,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -316,7 +316,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>Humann2Parser.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.wgs/Kraken2Parser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.wgs/Kraken2Parser/index.html
@@ -290,7 +290,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -299,7 +299,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>Kraken2Parser.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.wgs/KrakenParser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.wgs/KrakenParser/index.html
@@ -290,7 +290,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -299,7 +299,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>KrakenParser.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit.parser.wgs/Metaphlan2Parser/index.html b/docs/GENERATED/biolockj.module.implicit.parser.wgs/Metaphlan2Parser/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.implicit.qiime/BuildQiimeMapping/index.html b/docs/GENERATED/biolockj.module.implicit.qiime/BuildQiimeMapping/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/qimme_classifier:v1.3.12
+<pre><code>biolockjdevteam/qimme_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.implicit.qiime/MergeQiimeOtuTables/index.html b/docs/GENERATED/biolockj.module.implicit.qiime/MergeQiimeOtuTables/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/qimme_classifier:v1.3.12
+<pre><code>biolockjdevteam/qimme_classifier:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.implicit/Demultiplexer/index.html b/docs/GENERATED/biolockj.module.implicit/Demultiplexer/index.html
@@ -409,7 +409,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -418,7 +418,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>Demultiplexer.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit/ImportMetadata/index.html b/docs/GENERATED/biolockj.module.implicit/ImportMetadata/index.html
@@ -247,7 +247,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>
@@ -256,7 +256,7 @@ <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link
 <code>ImportMetadata.imageTag</code><br></p>
 <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">#</a></h2>
 <p>Module developed by Mike Sioda                 <br />
-BioLockJ v1.3.12</p>
+BioLockJ v1.3.13</p>
 
             </div>
           </div>

diff --git a/docs/GENERATED/biolockj.module.implicit/RegisterNumReads/index.html b/docs/GENERATED/biolockj.module.implicit/RegisterNumReads/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.report.humann2/AddMetadataToPathwayTables/index.html b/docs/GENERATED/biolockj.module.report.humann2/AddMetadataToPathwayTables/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>

diff --git a/docs/GENERATED/biolockj.module.report.humann2/RemoveLowPathwayCounts/index.html b/docs/GENERATED/biolockj.module.report.humann2/RemoveLowPathwayCounts/index.html
@@ -218,7 +218,7 @@ <h2 id="adds-modules">Adds modules<a class="headerlink" href="#adds-modules" tit
 <em>none found</em>                   </p>
 <h2 id="docker">Docker<a class="headerlink" href="#docker" title="Permanent link">#</a></h2>
 <p>If running in docker, this module will run in a docker container from this image:<br></p>
-<pre><code>biolockjdevteam/biolockj_controller:v1.3.12
+<pre><code>biolockjdevteam/biolockj_controller:v1.3.13
 </code></pre>
 
 <p>This can be modified using the following properties:<br>