Merge pull request #145 from Kudostoy0u/main

Updated documentation

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

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

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

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).
+	.. 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

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>

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"

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>