Update docs

Author: olliecheng

_includes/parameters.html

@@ -59,8 +59,7 @@ <h3>Pipeline parameters</h3>
       <td><code>differential_model</code></td>
       <td>
         Model to use to call differentially modified sites, as a comma-separated
-        list. Options: adaptive_binomial, homo_norm, hetero_norm, binomial,
-        beta_binomial (accepted:
+        list. (accepted:
         <code>adaptive_binomial</code
         >|<code>homo_norm</code>|<code>hetero_norm</code>|<code>binomial</code>|<code>beta_binomial</code>)
       </td>
@@ -90,28 +89,48 @@ <h3>Modification calling parameters</h3>
   </thead>
   <tbody>
     <tr>
-      <td><code>max_negative_prob</code></td>
+      <td><code>min_reads_per_sample</code></td>
       <td>
-        Negative modification sites with probability within [x, 0.5] will be
-        ignored
+        How many reads each sample should have at a site in order for the site
+        to be considered.
       </td>
-      <td>0.2</td>
+      <td>5</td>
     </tr>
     <tr>
-      <td><code>min_positive_prob</code></td>
+      <td><code>mod_threshold_dorado</code></td>
       <td>
-        Positive modification sites with probability within [0.5, x] will be
-        ignored
+        A passing threshold to use with Dorado data to determine a base
+        modification.
       </td>
-      <td>0.8</td>
+      <td>0.5</td>
     </tr>
     <tr>
-      <td><code>min_reads_per_sample</code></td>
+      <td><code>mod_filter_dorado</code></td>
       <td>
-        How many reads each sample should have at a site in order for the site
-        to be considered.
+        Reads with a modification probability within this interval will be
+        filtered out and not used in the Dorado model. The format should be
+        <code>a,b</code> i.e. <code>0.2,0.8</code>. By default, no filtering is
+        done.
       </td>
-      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td><code>mod_threshold_m6anet</code></td>
+      <td>
+        A passing threshold to use with m6Anet data to determine a base
+        modification.
+      </td>
+      <td>0.033379376</td>
+    </tr>
+    <tr>
+      <td><code>mod_filter_m6anet</code></td>
+      <td>
+        Reads with a modification probability within this interval will be
+        filtered out and not used in the m6Anet model. The format should be
+        <code>a,b</code> i.e. <code>0.2,0.8</code>. By default, no filtering is
+        done.
+      </td>
+      <td></td>
     </tr>
   </tbody>
 </table>

configuration.md

@@ -4,6 +4,19 @@ layout: default
 nav_order: 3
 ---
 
+<blockquote class="note">
+<strong>mako</strong> is in active development and not all features are supported yet. Key features that need to be implemented:
+
+<ul>
+<li>m6Anet support</li>
+<li>Certain QC visualisations, such as the metagene plot</li>
+<li>The <code>mod_threshold_dorado/m6anet</code> and <code>mod_filter_dorado/m6anet</code> parameters</li>
+</ul>
+
+Bug reports are highly welcome and we would greatly appreciate they be sent to our <a href="https://github.com/shimlab/mako/issues">GitHub Issues tracker</a>.
+
+</blockquote>
+
 ## Parameters
 
 {% include parameters.html %}

index.md

@@ -15,6 +15,9 @@ The software is written in Nextflow and utilises Docker/Singularity containerisa
 {: .highlight }
 **See [Getting Started](getting-started) for instructions on how to install and run the pipeline.**
 
+{: .note }
+**mako** is in active development and not all features are supported. See [Configuration](configuration) for a list of what features are in-progress.
+
 ---
 
 ![assets](./assets/diagram.svg)
@@ -23,12 +26,12 @@ The software is written in Nextflow and utilises Docker/Singularity containerisa
 
 ## Steps of the pipeline
 
-1. Basecalling with dorado
-2. Choice of modification caller:
-   1. Dorado
-   2. m6Anet
-3. Site-level aggregation, filtering, and selection
-4. Choice of differential analysis methods:
-   1. Linear mixed-effects models
-   2. Modkit
-5. Visualization of results
+1. Sample and read QC
+2. Site-level aggregation, filtering, and selection
+3. Choice of differential analysis methods:
+   1. Either binomial or beta-binomial, depending on the dispersion (**default**)
+   2. Binomial
+   3. Beta-binomial
+   4. Homoscedastic normal
+   5. Heteroscedastic normal
+4. Visualization of results via _makoview_