diff --git a/docs/_build/doctrees/documentation/workflow_reference/dependencies.doctree b/docs/_build/doctrees/documentation/workflow_reference/dependencies.doctree
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diff --git a/docs/_build/doctrees/documentation/workflow_reference/quick_start.doctree b/docs/_build/doctrees/documentation/workflow_reference/quick_start.doctree
index 02a20c9..07602d7 100644
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diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
index 3131e2a..f52ebc2 100644
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diff --git a/docs/_build/html/_sources/documentation/workflow_reference/dependencies.rst.txt b/docs/_build/html/_sources/documentation/workflow_reference/dependencies.rst.txt
index ec92861..84c50e7 100644
--- a/docs/_build/html/_sources/documentation/workflow_reference/dependencies.rst.txt
+++ b/docs/_build/html/_sources/documentation/workflow_reference/dependencies.rst.txt
@@ -3,7 +3,8 @@ Dependencies
 
 This workflow relies on the following tools being installed and accessible by your system PATH. We recommend that you install FinaleToolkit through ``pip`` and the other packages through ``conda`` in the Bioconda channel:
 
-* ``finaletoolkit``: A command-line tool for epigenomic analysis.
-* ``bedtools``: A suite of utilities for working with genomic intervals.
-* ``htslib``: A library that includes ``bgzip``, necessary to GZIP uncompressed BED files.
+* ``finaletoolkit``: A command-line tool for epigenomic feature extraction.
+* ``snakemake``: A workflow engine that determines which operations ("rules") to carry out on genomic files.
+* ``bedtools``: A suite of utilities for working with and manipulating genomic intervals.
+* ``htslib``: A library that includes ``bgzip```, necessary to GZIP uncompressed BED files. 
 * ``samtools``: A set of tools for manipulating and analyzing sequencing BAM/CRAM data
\ No newline at end of file
diff --git a/docs/_build/html/_sources/documentation/workflow_reference/index.rst.txt b/docs/_build/html/_sources/documentation/workflow_reference/index.rst.txt
index d1c4b32..04efde6 100644
--- a/docs/_build/html/_sources/documentation/workflow_reference/index.rst.txt
+++ b/docs/_build/html/_sources/documentation/workflow_reference/index.rst.txt
@@ -8,6 +8,7 @@ This Snakemake workflow automates the extraction of epigenomic features using Fi
    :caption: Contents:
 
    key_features
+   installation
    dependencies
    quick_start
    workflow_structure
diff --git a/docs/_build/html/_sources/documentation/workflow_reference/installation.rst.txt b/docs/_build/html/_sources/documentation/workflow_reference/installation.rst.txt
new file mode 100644
index 0000000..7929eb1
--- /dev/null
+++ b/docs/_build/html/_sources/documentation/workflow_reference/installation.rst.txt
@@ -0,0 +1,13 @@
+Installation
+------------
+
+Reference the following command for setup and execution:
+
+.. code-block:: console
+
+    $ git clone https://github.com/epifluidlab/finaletoolkit_workflow # Download the repository containing the workflow
+    $ cd finaletoolkit_workflow # Enter the repository folder
+    $ conda env create -f environment.yml # Create environment with relevant conda packages
+    $ conda activate finaletoolkit_workflow # Use environment for finaletoolkit-workflow
+    $ pip install finaletoolkit # Install finaletoolkit seperately through pip
+    $ snakemake --configfile params.yaml --cores 4 --jobs 2 # Run with parameters set in params.yaml
\ No newline at end of file
diff --git a/docs/_build/html/_sources/documentation/workflow_reference/quick_start.rst.txt b/docs/_build/html/_sources/documentation/workflow_reference/quick_start.rst.txt
index be4c1cc..137750c 100644
--- a/docs/_build/html/_sources/documentation/workflow_reference/quick_start.rst.txt
+++ b/docs/_build/html/_sources/documentation/workflow_reference/quick_start.rst.txt
@@ -1,10 +1,24 @@
 Quick Start
 -----------
 
-1.  **Configuration:**  Create a ``params.yaml`` file defining your input, output, and processing options (reference below sections).
-2.  **Basic Execution:** Run the workflow with ``snakemake --configfile params.yaml -c <cores> -j <jobs>``.
+*  **Configuration:**  Create a ``params.yaml`` file defining your input, output, and processing options (reference below sections).
 
-   * ``-c``: Number of CPU cores to use.
-   * ``-j``: Maximum number of concurrent jobs.
+*	**Basic Execution:** Once you're in the relevant folder with the ``Snakefile`` present, run the workflow through the following command:
 
-3.  **SLURM Execution:** Submit to SLURM to run in the background with ``snakemake --profile slurm_profile > snakemake.log 2>&1 &`` (see ``slurm_profile/config.yaml`` for default settings).
\ No newline at end of file
+	.. code-block:: bash
+ 
+		cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile
+
+		snakemake --configfile params.yaml --cores <cores> --jobs <jobs>
+		# --cores: Number of CPU cores to use.
+		# --jobs: Maximum number of concurrent jobs (limited by --cores).
+
+*	**SLURM Execution:** Submit to SLURM to run the workflow through the command below (see ``slurm_profile/config.yaml`` for default settings).
+
+	.. code-block:: bash
+
+		cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile
+      
+		snakemake  --profile slurm_profile > snakemake.log 2>&1 &
+		# Runs the command through params specified in slurm_profile/config.yaml in the background (&),
+		# Redirects all command-related output to snakemake.log
diff --git a/docs/_build/html/documentation/index.html b/docs/_build/html/documentation/index.html
index 1e826d5..d0f15d0 100644
--- a/docs/_build/html/documentation/index.html
+++ b/docs/_build/html/documentation/index.html
@@ -326,6 +326,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="workflow_reference/index.html">Workflow</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="workflow_reference/key_features.html">Key Features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflow_reference/installation.html">Installation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="workflow_reference/dependencies.html">Dependencies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="workflow_reference/quick_start.html">Quick Start</a></li>
 <li class="toctree-l2"><a class="reference internal" href="workflow_reference/workflow_structure.html">Workflow Structure</a></li>
diff --git a/docs/_build/html/documentation/workflow_reference/dependencies.html b/docs/_build/html/documentation/workflow_reference/dependencies.html
index dc27803..dc14c0b 100644
--- a/docs/_build/html/documentation/workflow_reference/dependencies.html
+++ b/docs/_build/html/documentation/workflow_reference/dependencies.html
@@ -46,7 +46,7 @@
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
     <link rel="next" title="Quick Start" href="quick_start.html" />
-    <link rel="prev" title="Key Features" href="key_features.html" />
+    <link rel="prev" title="Installation" href="installation.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   <meta name="docsearch:version" content="" />
@@ -304,6 +304,7 @@
   <div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="key_features.html">Key Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Dependencies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a></li>
 <li class="toctree-l1"><a class="reference internal" href="workflow_structure.html">Workflow Structure</a></li>
@@ -380,9 +381,10 @@
 <h1>Dependencies<a class="headerlink" href="#dependencies" title="Link to this heading">#</a></h1>
 <p>This workflow relies on the following tools being installed and accessible by your system PATH. We recommend that you install FinaleToolkit through <code class="docutils literal notranslate"><span class="pre">pip</span></code> and the other packages through <code class="docutils literal notranslate"><span class="pre">conda</span></code> in the Bioconda channel:</p>
 <ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">finaletoolkit</span></code>: A command-line tool for epigenomic analysis.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">bedtools</span></code>: A suite of utilities for working with genomic intervals.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">htslib</span></code>: A library that includes <code class="docutils literal notranslate"><span class="pre">bgzip</span></code>, necessary to GZIP uncompressed BED files.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">finaletoolkit</span></code>: A command-line tool for epigenomic feature extraction.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">snakemake</span></code>: A workflow engine that determines which operations (“rules”) to carry out on genomic files.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">bedtools</span></code>: A suite of utilities for working with and manipulating genomic intervals.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">htslib</span></code>: A library that includes <code class="docutils literal notranslate"><span class="pre">bgzip`</span></code>, necessary to GZIP uncompressed BED files.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">samtools</span></code>: A set of tools for manipulating and analyzing sequencing BAM/CRAM data</p></li>
 </ul>
 </section>
@@ -398,12 +400,12 @@ <h1>Dependencies<a class="headerlink" href="#dependencies" title="Link to this h
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="key_features.html"
+       href="installation.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Key Features</p>
+        <p class="prev-next-title">Installation</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/docs/_build/html/documentation/workflow_reference/index.html b/docs/_build/html/documentation/workflow_reference/index.html
index fc3fd35..445862f 100644
--- a/docs/_build/html/documentation/workflow_reference/index.html
+++ b/docs/_build/html/documentation/workflow_reference/index.html
@@ -304,6 +304,7 @@
   <div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="key_features.html">Key Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dependencies.html">Dependencies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a></li>
 <li class="toctree-l1"><a class="reference internal" href="workflow_structure.html">Workflow Structure</a></li>
@@ -380,6 +381,7 @@ <h1>Workflow<a class="headerlink" href="#workflow" title="Link to this heading">
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="key_features.html">Key Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dependencies.html">Dependencies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a></li>
 <li class="toctree-l1"><a class="reference internal" href="workflow_structure.html">Workflow Structure</a></li>
diff --git a/docs/_build/html/documentation/workflow_reference/installation.html b/docs/_build/html/documentation/workflow_reference/installation.html
new file mode 100644
index 0000000..dcfcd55
--- /dev/null
+++ b/docs/_build/html/documentation/workflow_reference/installation.html
@@ -0,0 +1,498 @@
+
+<!DOCTYPE html>
+
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+<html lang="en" data-content_root="../../" >
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  
+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
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+  
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+  
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+  <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
+  <div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="key_features.html">Key Features</a></li>
+<li class="toctree-l1 current active"><a class="current reference internal" href="#">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dependencies.html">Dependencies</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflow_structure.html">Workflow Structure</a></li>
+<li class="toctree-l1"><a class="reference internal" href="yaml_parameters.html">YAML Parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="output_file_naming.html">Output File Naming</a></li>
+<li class="toctree-l1"><a class="reference internal" href="finaletoolkit_commands.html">Using Finaletoolkit Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="mappability_filtering.html">Mappability Filtering</a></li>
+<li class="toctree-l1"><a class="reference internal" href="filter_file.html"><code class="docutils literal notranslate"><span class="pre">filter-file</span></code> Command</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notes.html">Notes</a></li>
+</ul>
+</div>
+</nav></div>
+    </div>
+  
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+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
+  </div>
+
+
+      </div>
+      
+      <main id="main-content" class="bd-main" role="main">
+        
+        
+          <div class="bd-content">
+            <div class="bd-article-container">
+              
+              <div class="bd-header-article d-print-none">
+<div class="header-article-items header-article__inner">
+  
+    <div class="header-article-items__start">
+      
+        <div class="header-article-item">
+
+<nav aria-label="Breadcrumb" class="d-print-none">
+  <ul class="bd-breadcrumbs">
+    
+    <li class="breadcrumb-item breadcrumb-home">
+      <a href="../../index.html" class="nav-link" aria-label="Home">
+        <i class="fa-solid fa-home"></i>
+      </a>
+    </li>
+    
+    <li class="breadcrumb-item"><a href="../index.html" class="nav-link">FinaleToolkit Documentation</a></li>
+    
+    
+    <li class="breadcrumb-item"><a href="index.html" class="nav-link">Workflow</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page"><span class="ellipsis">Installation</span></li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
+  
+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="installation">
+<h1>Installation<a class="headerlink" href="#installation" title="Link to this heading">#</a></h1>
+<p>Reference the following command for setup and execution:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/epifluidlab/finaletoolkit_workflow<span class="w"> </span><span class="c1"># Download the repository containing the workflow</span>
+<span class="gp">$ </span><span class="nb">cd</span><span class="w"> </span>finaletoolkit_workflow<span class="w"> </span><span class="c1"># Enter the repository folder</span>
+<span class="gp">$ </span>conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>-f<span class="w"> </span>environment.yml<span class="w"> </span><span class="c1"># Create environment with relevant conda packages</span>
+<span class="gp">$ </span>conda<span class="w"> </span>activate<span class="w"> </span>finaletoolkit_workflow<span class="w"> </span><span class="c1"># Use environment for finaletoolkit-workflow</span>
+<span class="gp">$ </span>pip<span class="w"> </span>install<span class="w"> </span>finaletoolkit<span class="w"> </span><span class="c1"># Install finaletoolkit seperately through pip</span>
+<span class="gp">$ </span>snakemake<span class="w"> </span>--configfile<span class="w"> </span>params.yaml<span class="w"> </span>--cores<span class="w"> </span><span class="m">4</span><span class="w"> </span>--jobs<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="c1"># Run with parameters set in params.yaml</span>
+</pre></div>
+</div>
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer d-print-none">
+                  
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+    <a class="left-prev"
+       href="key_features.html"
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+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
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+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation/workflow_reference/installation.rst.txt"
+            rel="nofollow">Show Source</a></li>
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+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
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+<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
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+<div class="bd-footer__inner bd-page-width">
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+    <div class="footer-items__start">
+      
+        <div class="footer-item">
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+    
+      © Copyright 2024, EpiFluidLab.
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+        <div class="footer-item">
+
+  <p class="sphinx-version">
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.1.3.
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diff --git a/docs/_build/html/documentation/workflow_reference/quick_start.html b/docs/_build/html/documentation/workflow_reference/quick_start.html
index c3e8d21..c019838 100644
--- a/docs/_build/html/documentation/workflow_reference/quick_start.html
+++ b/docs/_build/html/documentation/workflow_reference/quick_start.html
@@ -304,6 +304,7 @@
   <div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="key_features.html">Key Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dependencies.html">Dependencies</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Quick Start</a></li>
 <li class="toctree-l1"><a class="reference internal" href="workflow_structure.html">Workflow Structure</a></li>
@@ -378,19 +379,27 @@
                   
   <section id="quick-start">
 <h1>Quick Start<a class="headerlink" href="#quick-start" title="Link to this heading">#</a></h1>
-<ol class="arabic simple">
+<ul>
 <li><p><strong>Configuration:</strong>  Create a <code class="docutils literal notranslate"><span class="pre">params.yaml</span></code> file defining your input, output, and processing options (reference below sections).</p></li>
-<li><p><strong>Basic Execution:</strong> Run the workflow with <code class="docutils literal notranslate"><span class="pre">snakemake</span> <span class="pre">--configfile</span> <span class="pre">params.yaml</span> <span class="pre">-c</span> <span class="pre">&lt;cores&gt;</span> <span class="pre">-j</span> <span class="pre">&lt;jobs&gt;</span></code>.</p></li>
-</ol>
-<blockquote>
-<div><ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">-c</span></code>: Number of CPU cores to use.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">-j</span></code>: Maximum number of concurrent jobs.</p></li>
+<li><p><strong>Basic Execution:</strong> Once you’re in the relevant folder with the <code class="docutils literal notranslate"><span class="pre">Snakefile</span></code> present, run the workflow through the following command:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>finaletoolkit_workflow<span class="w"> </span><span class="c1"># Enter the folder with the workflow Snakefile</span>
+
+snakemake<span class="w"> </span>--configfile<span class="w"> </span>params.yaml<span class="w"> </span>--cores<span class="w"> </span>&lt;cores&gt;<span class="w"> </span>--jobs<span class="w"> </span>&lt;jobs&gt;
+<span class="c1"># --cores: Number of CPU cores to use.</span>
+<span class="c1"># --jobs: Maximum number of concurrent jobs (limited by --cores).</span>
+</pre></div>
+</div>
+</li>
+<li><p><strong>SLURM Execution:</strong> Submit to SLURM to run the workflow through the command below (see <code class="docutils literal notranslate"><span class="pre">slurm_profile/config.yaml</span></code> for default settings).</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>finaletoolkit_workflow<span class="w"> </span><span class="c1"># Enter the folder with the workflow Snakefile</span>
+
+snakemake<span class="w">  </span>--profile<span class="w"> </span>slurm_profile<span class="w"> </span>&gt;<span class="w"> </span>snakemake.log<span class="w"> </span><span class="m">2</span>&gt;<span class="p">&amp;</span><span class="m">1</span><span class="w"> </span><span class="p">&amp;</span>
+<span class="c1"># Runs the command through params specified in slurm_profile/config.yaml in the background (&amp;),</span>
+<span class="c1"># Redirects all command-related output to snakemake.log</span>
+</pre></div>
+</div>
+</li>
 </ul>
-</div></blockquote>
-<ol class="arabic simple" start="3">
-<li><p><strong>SLURM Execution:</strong> Submit to SLURM to run in the background with <code class="docutils literal notranslate"><span class="pre">snakemake</span> <span class="pre">--profile</span> <span class="pre">slurm_profile</span> <span class="pre">&gt;</span> <span class="pre">snakemake.log</span> <span class="pre">2&gt;&amp;1</span> <span class="pre">&amp;</span></code> (see <code class="docutils literal notranslate"><span class="pre">slurm_profile/config.yaml</span></code> for default settings).</p></li>
-</ol>
 </section>
 
 
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 76c7c9f..9e90ef1 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -379,6 +379,7 @@ <h2>Documentation<a class="headerlink" href="#documentation" title="Link to this
 </li>
 <li class="toctree-l1"><a class="reference internal" href="documentation/workflow_reference/index.html">Workflow</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="documentation/workflow_reference/key_features.html">Key Features</a></li>
+<li class="toctree-l2"><a class="reference internal" href="documentation/workflow_reference/installation.html">Installation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="documentation/workflow_reference/dependencies.html">Dependencies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="documentation/workflow_reference/quick_start.html">Quick Start</a></li>
 <li class="toctree-l2"><a class="reference internal" href="documentation/workflow_reference/workflow_structure.html">Workflow Structure</a></li>
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 24a09d4..4b82dbc 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 2155d80..bb7e050 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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"Installation": [[14, null], [14, "id1"]], "Intersect Policy": [[15, null]], "Introduction": [[18, null]], "Key Features": [[23, null]], "License": [[30, "license"]], "Mappability Filtering": [[24, null]], "Midpoint": [[15, "midpoint"]], "Motif Diversity Score (MDS)": [[10, "motif-diversity-score-mds"]], "Named Arguments": [[8, "finaletoolkit.cli.main_cli-main_cli_parser-named-arguments"], [8, "named-arguments"], [8, "named-arguments_repeat1"], [8, "named-arguments_repeat2"], [8, "named-arguments_repeat3"], [8, "named-arguments_repeat4"], [8, "named-arguments_repeat5"], [8, "named-arguments_repeat6"], [8, "named-arguments_repeat7"], [8, "named-arguments_repeat8"], [8, "named-arguments_repeat9"], [8, "named-arguments_repeat10"], [8, "named-arguments_repeat11"], [8, "named-arguments_repeat12"], [8, "named-arguments_repeat13"]], "Notes": [[25, null]], "Output File Naming": [[26, null]], "Positional Arguments": [[8, "positional-arguments"], [8, "positional-arguments_repeat1"], [8, 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"FinaleToolkit"], "titleterms": {"about": 31, "adjust": 8, "agg": 8, "ani": 15, "api": 6, "argument": 8, "bam": 13, "basic": 0, "bed": 8, "bin": 8, "bw": 8, "citat": 31, "cleavag": [1, 8, 10], "cli": 8, "command": [8, 20, 21], "contact": 31, "content": 22, "correct": 8, "coverag": [8, 10], "cram": 13, "data": 13, "delfi": [2, 8, 10], "depend": 19, "divers": 10, "document": [9, 31], "end": [3, 8, 10], "error": 14, "featur": [0, 10, 24], "file": [4, 8, 13, 20, 27], "filter": [8, 20, 25], "finaletoolkit": [9, 21, 31], "frag": [4, 8], "fragment": [10, 13], "gap": 8, "gc": 8, "genom": 5, "get": 16, "guid": 12, "help": 11, "import": 16, "input": 13, "instal": [14, 23], "intersect": 15, "interv": 8, "introduct": 18, "kei": 24, "length": [8, 10], "licens": 31, "mappabl": 25, "md": [8, 10], "midpoint": 15, "modul": 16, "motif": [3, 8, 10], "name": [8, 27], "note": 26, "output": 27, "paramet": 30, "polici": 15, "posit": 8, "prerequisit": 14, "profil": [1, 8, 10], "protect": [7, 10], "quick": 28, 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\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 34f2df7..6908ce3 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -19,7 +19,7 @@
 extensions = [
     'sphinx.ext.autodoc',
     'sphinxarg.ext',
-    'sphinx.ext.napoleon'
+    'sphinx.ext.napoleon',
 ]
 
 # -- Options for HTML output -------------------------------------------------
diff --git a/docs/documentation/workflow_reference/dependencies.rst b/docs/documentation/workflow_reference/dependencies.rst
index ec92861..84c50e7 100644
--- a/docs/documentation/workflow_reference/dependencies.rst
+++ b/docs/documentation/workflow_reference/dependencies.rst
@@ -3,7 +3,8 @@ Dependencies
 
 This workflow relies on the following tools being installed and accessible by your system PATH. We recommend that you install FinaleToolkit through ``pip`` and the other packages through ``conda`` in the Bioconda channel:
 
-* ``finaletoolkit``: A command-line tool for epigenomic analysis.
-* ``bedtools``: A suite of utilities for working with genomic intervals.
-* ``htslib``: A library that includes ``bgzip``, necessary to GZIP uncompressed BED files.
+* ``finaletoolkit``: A command-line tool for epigenomic feature extraction.
+* ``snakemake``: A workflow engine that determines which operations ("rules") to carry out on genomic files.
+* ``bedtools``: A suite of utilities for working with and manipulating genomic intervals.
+* ``htslib``: A library that includes ``bgzip```, necessary to GZIP uncompressed BED files. 
 * ``samtools``: A set of tools for manipulating and analyzing sequencing BAM/CRAM data
\ No newline at end of file
diff --git a/docs/documentation/workflow_reference/index.rst b/docs/documentation/workflow_reference/index.rst
index d1c4b32..04efde6 100644
--- a/docs/documentation/workflow_reference/index.rst
+++ b/docs/documentation/workflow_reference/index.rst
@@ -8,6 +8,7 @@ This Snakemake workflow automates the extraction of epigenomic features using Fi
    :caption: Contents:
 
    key_features
+   installation
    dependencies
    quick_start
    workflow_structure
diff --git a/docs/documentation/workflow_reference/installation.rst b/docs/documentation/workflow_reference/installation.rst
new file mode 100644
index 0000000..7929eb1
--- /dev/null
+++ b/docs/documentation/workflow_reference/installation.rst
@@ -0,0 +1,13 @@
+Installation
+------------
+
+Reference the following command for setup and execution:
+
+.. code-block:: console
+
+    $ git clone https://github.com/epifluidlab/finaletoolkit_workflow # Download the repository containing the workflow
+    $ cd finaletoolkit_workflow # Enter the repository folder
+    $ conda env create -f environment.yml # Create environment with relevant conda packages
+    $ conda activate finaletoolkit_workflow # Use environment for finaletoolkit-workflow
+    $ pip install finaletoolkit # Install finaletoolkit seperately through pip
+    $ snakemake --configfile params.yaml --cores 4 --jobs 2 # Run with parameters set in params.yaml
\ No newline at end of file
diff --git a/docs/documentation/workflow_reference/quick_start.rst b/docs/documentation/workflow_reference/quick_start.rst
index be4c1cc..137750c 100644
--- a/docs/documentation/workflow_reference/quick_start.rst
+++ b/docs/documentation/workflow_reference/quick_start.rst
@@ -1,10 +1,24 @@
 Quick Start
 -----------
 
-1.  **Configuration:**  Create a ``params.yaml`` file defining your input, output, and processing options (reference below sections).
-2.  **Basic Execution:** Run the workflow with ``snakemake --configfile params.yaml -c <cores> -j <jobs>``.
+*  **Configuration:**  Create a ``params.yaml`` file defining your input, output, and processing options (reference below sections).
 
-   * ``-c``: Number of CPU cores to use.
-   * ``-j``: Maximum number of concurrent jobs.
+*	**Basic Execution:** Once you're in the relevant folder with the ``Snakefile`` present, run the workflow through the following command:
 
-3.  **SLURM Execution:** Submit to SLURM to run in the background with ``snakemake --profile slurm_profile > snakemake.log 2>&1 &`` (see ``slurm_profile/config.yaml`` for default settings).
\ No newline at end of file
+	.. code-block:: bash
+ 
+		cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile
+
+		snakemake --configfile params.yaml --cores <cores> --jobs <jobs>
+		# --cores: Number of CPU cores to use.
+		# --jobs: Maximum number of concurrent jobs (limited by --cores).
+
+*	**SLURM Execution:** Submit to SLURM to run the workflow through the command below (see ``slurm_profile/config.yaml`` for default settings).
+
+	.. code-block:: bash
+
+		cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile
+      
+		snakemake  --profile slurm_profile > snakemake.log 2>&1 &
+		# Runs the command through params specified in slurm_profile/config.yaml in the background (&),
+		# Redirects all command-related output to snakemake.log