Formatting updates

Author: asaravia-butler

GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/README.md

@@ -10,11 +10,11 @@
       - [Step 1: Install Singularity](#step-1-install-singularity)
       - [Step 2: Fetch the Singularity Image](#step-2-fetch-the-singularity-image)
       - [Step 3: Run the Workflow](#step-3-run-the-workflow)
-      - [Step 4: Run the Annotations Database Creation Function as a Stand-Alone Script](#step-4-run-the-annotations-database-creation-function-as-a-stand-alone-script)
+      - [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script)
     - [Approach 2: Using a Local R Environment](#approach-2-using-a-local-r-environment)
       - [Step 1: Install R and Required R Packages](#step-1-install-r-and-required-r-packages)
       - [Step 2: Run the Workflow](#step-2-run-the-workflow)
-      - [Step 3: Run the Annotations Database Creation Function as a Stand-Alone Script](#step-3-run-the-annotations-database-creation-function-as-a-stand-alone-script)
+      - [Optional: Run the Annotations Database Creation Function as a Stand-Alone Script](#optional-run-the-annotations-database-creation-function-as-a-stand-alone-script)
 
 <br> 
 
@@ -52,35 +52,42 @@ The GL_RefAnnotTable-A workflow can be run using one of two approaches:
 
 Please follow the instructions for the approach that best matches your setup and preferences. Each method is explained in detail below. 
 
+<br> 
+
 ---
 
 ### Approach 1: Using Singularity
 
 This approach allows you to run the workflow within a containerized environment, ensuring consistency and reproducibility.
 
+<br>
+
 #### Step 1: Install Singularity
 
 Singularity is a containerization platform for running applications portably and reproducibly. We use container images hosted on Quay.io to encapsulate all the necessary software and dependencies required by the GL_RefAnnotTable-A workflow. This setup allows you to run the workflow without installing any software directly on your system. 
+  
 > ***Note**: Other containerization tools like Docker or Apptainer can also be used to pull and run these images.*
+   
 
-We recommend installing Singularity system-wide as per the official [Singularity installation documentation](https://docs.sylabs.io/guides/3.10/admin-guide/admin_quickstart.html).
+We recommend installing Singularity system-wide as per the official [Singularity installation documentation](https://docs.sylabs.io/guides/3.10/admin-guide/admin_quickstart.html).  
+ 
 
 > ***Note**: While Singularity is also available through [Anaconda](https://anaconda.org/conda-forge/singularity), we recommend installing Singularity system-wide following the official installation documentation.*
 
 <br> 
 
 #### Step 2: Fetch the Singularity Image
 
-To pull the Singularity image needed for the workflow, you can use the provided script as directed below or pull the image directly.
+To pull the Singularity image needed for the workflow, you can use the provided script as directed below or pull the image directly.  
 
-> ***Note**: This command should be run in the location containing the `GL_RefAnnotTable-A_1.1.0` directory that was downloaded in [step 1](#1-download-the-workflow-files). Depending on your network speed, fetching the images will take approximately 20 minutes.*
+> ***Note**: This command should be run in the location containing the `GL_RefAnnotTable-A_1.1.0` directory that was downloaded in [step 1](#1-download-the-workflow-files). Depending on your network speed, fetching the images will take approximately 20 minutes.*  
  
 
 ```bash
 bash GL_RefAnnotTable-A_1.1.0/bin/prepull_singularity.sh GL_RefAnnotTable-A_1.1.0/config/software/by_docker_image.config
 ```
 
-Once complete, a `singularity` folder containing the Singularity images will be created. Run the following command to export this folder as an environment variable: 
+Once complete, a `singularity` folder containing the Singularity images will be created. Run the following command to export this folder as an environment variable:  
 
 
 ```bash
@@ -98,13 +105,14 @@ singularity exec -B $(pwd)/GL_RefAnnotTable-A_1.1.0:/work \
 $SINGULARITY_CACHEDIR/quay.io-nasa_genelab-gl-refannottable-a-1.1.0.img \
 Rscript /work/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus musculus'
 ```
- 
+<br> 
+
 **Input data:**
 
 - No input files are required. Specify the species name of the target organism using a positional command line argument. `Mus musculus` is used in the example above.
-  > **Notes**:
-  > To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
-  > The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)  
+  > **Notes**:  
+  > - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.  
+  > - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)  
 - *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.  
 
 
@@ -117,7 +125,7 @@ Rscript /work/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus musculus'
 
 #### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script
 
-If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script: 
+If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script:  
 
 
 ```bash
@@ -126,11 +134,12 @@ $SINGULARITY_CACHEDIR/quay.io-nasa_genelab-gl-refannottable-a-1.1.0.img \
 Rscript /work/install-org-db.R 'Bacillus subtilis'
 ```
 
+<br>
 
 **Input data:**
 
-- The species name of the target organism must be specified as the first positional command line argument. `Bacillus subtilis` is used in the example above.
-  > **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)  
+- The species name of the target organism must be specified as the first positional command line argument. `Bacillus subtilis` is used in the example above.  
+  > **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)   
 - *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.  
 
 
@@ -146,6 +155,8 @@ Rscript /work/install-org-db.R 'Bacillus subtilis'
 
 This approach allows you to run the workflow directly in your local R environment without using containers.
 
+<br>
+
 #### Step 1: Install R and Required R Packages
 
 We recommend installing R via the [Comprehensive R Archive Network (CRAN)](https://cran.r-project.org/):
@@ -184,20 +195,21 @@ BiocManager::install("GO.db")
 
 #### Step 2: Run the Workflow
 
-While in the directory containing the `GL_RefAnnotTable-A_1.1.0` folder, you can now run the workflow. Below is an example of how to run the workflow to build an annotation table for *Mus musculus* (mouse): 
+While in the directory containing the `GL_RefAnnotTable-A_1.1.0` folder, you can now run the workflow. Below is an example of how to run the workflow to build an annotation table for *Mus musculus* (mouse):  
 
 
 ```bash
 Rscript GL_RefAnnotTable-A_1.1.0/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus musculus'
 ```
- 
+
+ <br> 
 
 **Input data:**
 
 - No input files are required. Specify the species name of the target organism using a positional command line argument. `Mus musculus` is used in the example above.
-  > **Notes**:
-  > To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
-  > The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)  
+  > **Notes**:  
+  > - To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments.
+  > - The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)   
 - *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.
 
 
@@ -210,17 +222,19 @@ Rscript GL_RefAnnotTable-A_1.1.0/GL-DPPD-7110-A_build-genome-annots-tab.R 'Mus m
 
 #### *Optional*: Run the Annotations Database Creation Function as a Stand-Alone Script
 
-If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script: 
+If the reference table does not specify an annotations database for the target organism in the 'annotations' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) file, the `install_annotations` function (defined in `install-org-db.R`) will be executed by default. This function can also be run as a stand-alone script:  
 
 
 ```bash
 Rscript GL_RefAnnotTable-A_1.1.0/install-org-db.R 'Bacillus subtilis'
 ```
 
+<br>
+
 **Input data:**
 
 - The species name of the target organism must be specified as the first positional command line argument. `Bacillus subtilis` is used in the example above.
-  > **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)  
+  > **Note**: The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)   
 - *Optional*: A local reference table CSV file can be supplied as a second positional argument. If not provided, the script will download the current version of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) table by default.