Update README.md

README.md

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 # HPC Nextflow / nf-core Pipeline Setup
 
-This repository provides instructions for setting up and running Nextflow-based nf-core pipelines on a High-Performance Computing (HPC) system. The setup process has been tailored for UCLA's Hoffman2 cluster. However, SGE clusters will have similar installation steps.
+This repository provides instructions for setting up and running Nextflow-based nf-core pipelines on a High-Performance Computing (HPC) system. The setup process has been tailored for UCLA's Hoffman2 cluster. However, SGE clusters will follow similar installation steps. Alternatively, use the bash setup file for a more straightforward setup.
 
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 ## Prerequisites
 
 - HPC Access: Ensure you have valid login credentials and the necessary permissions.
+
+
+## Setup File Execution
+Step 1: Login and spin up a node on your cluster
+```
+qrsh -l h_data=15G,h_rt=3:00:00,h_vmem=4G -pe shared 4
+```
+<br />Step 2: Upload the nextflow_setup.sh file to the desired directory
+<br />Step 3: cd into the directory where the nextflow_setup.sh bash script lives
+<br />Step 4: Execute the bash script by running the following code
+```
+bash nextflow_setup.sh
+```