diff --git a/README.md b/README.md index 1149f80..bcf9ffa 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,22 @@ # 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. If you find this documentation useful, please consider leaving feedback! ## 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 +``` +
Step 2: Upload the nextflow_setup.sh file to the desired directory +
Step 3: cd into the directory where the nextflow_setup.sh bash script lives +
Step 4: Execute the bash script by running the following code +``` +bash nextflow_setup.sh +```