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nf-core/configs: Newcastle HPC Configuration

Configuration for the Newcastle high performance computing (HPC) cluster.

Setup

To install nextflow we first need to get the prequisite java from module avail:

module load Java/17.0.6

Then installing Nextflow using the standard install options: https://www.nextflow.io/docs/latest/install.html

curl -s https://get.nextflow.io | bash

Make Nextflow executable:

chmod +x nextflow

Then move Nextflow into an executable path. For example:

mkdir -p $HOME/bin/ mv nextflow $HOME/bin/

To ensure this works every time you login to the cluster, put inside your ~/.bash_profile the java install:

nano ~/.bash_profile

Then paste in the line for the java install:

#Java module add v17:
module load Java/17.0.6

Exit nano with, control-X, then y to save, then enter to confirm

Run

To use this profile, simply pass Nextflow the -profile newcastle flag eg.

nextflow run nf-core/_pipeline_ -profile newcastle --outdir results

In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) at ecoflow.ucl@gmail.com . We are based at UCL, but helped set up this config, and are happy to help.
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