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Guide to setting up nextflow / nf-core pipelines on HPC clusters

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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 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.

Straightforward Setup

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

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