Deployed b6c1ae0 with MkDocs version: 1.6.1

index.html

@@ -284,5 +284,5 @@ <h2 id="citations">Citations</h2>
 
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 MkDocs version : 1.6.1
-Build Date UTC : 2024-12-03 17:30:23.465749+00:00
+Build Date UTC : 2024-12-08 09:21:39.823771+00:00
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params/index.html

@@ -485,23 +485,23 @@ <h2 id="download-entry">Download Entry</h2>
 <tbody>
 <tr>
 <td><code>download_functional</code></td>
-<td>Whether to dowload functional references</td>
+<td>Whether to download functional references</td>
 <td><code>boolean</code></td>
 <td>True</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td><code>download_kaiju</code></td>
-<td>Whether to dowload the Kaiju reference db</td>
+<td>Whether to download the Kaiju reference db</td>
 <td><code>boolean</code></td>
 <td>True</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td><code>download_kraken</code></td>
-<td>Whether to dowload the Kraken2 reference db</td>
+<td>Whether to download the Kraken2 reference db</td>
 <td><code>boolean</code></td>
 <td></td>
 <td></td>

usage/index.html

@@ -214,7 +214,7 @@ <h3 id="-profile"><code>-profile</code></h3>
 </blockquote>
 <p>Note that multiple profiles can be loaded, for example: <code>-profile test,docker</code> - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.</p>
-<p>If <code>-profile</code> is not specified, the pipeline will run locally and expect all software to be installed and available on the <code>PATH</code>. This is <em>not</em> recommended, since it can lead to different results on different machines dependent on the computer enviroment.</p>
+<p>If <code>-profile</code> is not specified, the pipeline will run locally and expect all software to be installed and available on the <code>PATH</code>. This is <em>not</em> recommended, since it can lead to different results on different machines dependent on the computer environment.</p>
 <ul>
 <li><code>test</code></li>
 <li>A profile with a complete configuration for automated testing</li>
@@ -272,7 +272,7 @@ <h3 id="resource-requests">Resource requests</h3>
 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 </code></pre>
 <h4 id="for-beginners">For beginners</h4>
-<p>A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters <code>--max_cpus</code>, <code>--max_memory</code>, and <code>--max_time</code>. Based on the error above, you have to increase the amount of memory. Therefore you can go to the <a href="https://nf-co.re/rnaseq/3.9/parameters">parameter documentation of rnaseq</a> and scroll down to the <code>show hidden parameter</code> button to get the default value for <code>--max_memory</code>. In this case 128GB, you than can try to run your pipeline again with <code>--max_memory 200GB -resume</code> to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.</p>
+<p>A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefore you can try to increase the resource for the parameters <code>--max_cpus</code>, <code>--max_memory</code>, and <code>--max_time</code>. Based on the error above, you have to increase the amount of memory. Therefore you can go to the <a href="https://nf-co.re/rnaseq/3.9/parameters">parameter documentation of rnaseq</a> and scroll down to the <code>show hidden parameter</code> button to get the default value for <code>--max_memory</code>. In this case 128GB, you than can try to run your pipeline again with <code>--max_memory 200GB -resume</code> to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.</p>
 <h4 id="advanced-option-on-process-level">Advanced option on process level</h4>
 <p>To bypass this error you would need to find exactly which resources are set by the <code>DIAMOND_BLASTX</code> process. The quickest way is to search for <code>process DIAMOND_BLASTX</code> in the <a href="https://github.com/dalmolingroup/euryale/search?q=process+DIAMOND_BLASTX">dalmolingroup/euryale Github repo</a>.
 We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the <code>modules/</code> directory and so, based on the search results, the file we want is <code>modules/nf-core/diamond/blastx/main.nf</code>.