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faq/index.html

@@ -54,6 +54,8 @@
     </li>
     <li class="toctree-l2"><a class="reference internal" href="#can-i-use-the-arete-outputs-in-microreact">Can I use the ARETE outputs in MicroReact?</a>
     </li>
+    <li class="toctree-l2"><a class="reference internal" href="#why-am-i-getting-this-docker-permission-denied-error">Why am I getting this 'docker: Permission denied' error?</a>
+    </li>
     </ul>
                 </li>
               </ul>
@@ -161,6 +163,17 @@ <h2 id="can-i-use-the-arete-outputs-in-microreact">Can I use the ARETE outputs i
 <pre><code class="language-bash">gunzip feature_profile.tsv.gz
 </code></pre>
 <p>Make sure to check our <a href="https://beiko-lab.github.io/arete/output/">output documentation</a> for a full list of outputs and the <a href="https://beiko-lab.github.io/arete/params/">parameter documentation</a> for a description of parameters to enable and disable these outputs.</p>
+<h2 id="why-am-i-getting-this-docker-permission-denied-error">Why am I getting this 'docker: Permission denied' error?</h2>
+<p>Although previous ARETE users have reported this issue, this is neither an issue with Nextflow nor with ARETE itself.</p>
+<p>This is most likely due to how Docker permissions are set up on your machine.</p>
+<ul>
+<li>
+<p>If running on your own machine, take a look at <a href="https://docs.docker.com/engine/install/linux-postinstall/">this guide</a>.</p>
+</li>
+<li>
+<p>If running on an HPC system, talk to your system administrator or consider running ARETE with <a href="https://beiko-lab.github.io/arete/usage/#-profile">Singularity</a>.</p>
+</li>
+</ul>
 
             </div>
           </div><footer>

index.html

@@ -205,10 +205,11 @@ <h2 id="quick-start">Quick Start <a name="quickstart"></a></h2>
   --input_sample_table samplesheet.csv \
   --poppunk_model bgmm
 </code></pre>
-<p><code>samplesheet.csv</code> must be formatted <code>sample,fastq_1,fastq_2</code></p>
+<p><code>samplesheet.csv</code> must be formatted <code>sample,fastq_1,fastq_2</code>, with the first column being sample names and the other two corresponding to compressed FASTQ files.</p>
 <p><strong>Note</strong>: If you get this error at the end <code>Failed to invoke `workflow.onComplete` event handler</code> it isn't a problem, it just means you don't have an sendmail configured and it can't send an email report saying it finished correctly i.e., its not that the workflow failed.</p>
 <p>See <a href="https://beiko-lab.github.io/arete/usage/">usage docs</a> for all of the available options when running the pipeline.
-See the <a href="https://beiko-lab.github.io/arete/params/">parameter docs</a> for a list of all params currently implemented in the pipeline and which ones are required.</p>
+See the <a href="https://beiko-lab.github.io/arete/params/">parameter docs</a> for a list of all parameters currently implemented in the pipeline and which ones are required.
+See the <a href="https://beiko-lab.github.io/arete/faq/">FAQ</a> for a list of frequently asked questions and common issues.</p>
 <h3 id="testing">Testing</h3>
 <p>To test the worklow on a minimal dataset you can use the test configuration (with either docker or singularity - replace <code>docker</code> below as appropriate):</p>
 <pre><code class="language-bash">nextflow run beiko-lab/ARETE -profile test,docker
@@ -351,5 +352,5 @@ <h2 id="citing-arete">Citing ARETE <a name="citing"></a></h2>
 
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