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How to change default configuration

If you want to calculate many polygenic scores for a very large dataset (e.g. UK Biobank) you will likely need to adjust the pipeline settings. You might have access to a powerful workstation, a University cluster, or some cloud compute resources. This section will show how to set up pgsc_calc to submit work to these types of systems by creating and editing nextflow configuration files.

Example: allocate more RAM to loading and scoring processes​

process {
   withName: PGSC_CALC_LOAD {
       cpus = 2
       memory = "32.GB"
       time = "24.h"
   }
   withName: PGSC_CALC_SCORE {
       cpus = 2
       memory = "32.GB"
       time = "24.h"
   }   
}
warning

For larger jobs requesting more memory and time can be useful, but allocating more than 2-4 CPUs is rarely helpful.

Save this file as my_custom_config.config and include it using Nextflow's -c parameter:

$ nextflow run pgscatalog/pgsc_calc -r v3-alpha.1 -c my_custom_config ...

Example: HPC cluster (SLURM)​

If you have access to a HPC cluster, you'll need to configure your cluster's unique parameters to set correct queues, user accounts, and resource limits.

tip

You probably want to use -profile singularity/apptainer on a HPC

process {
    executor = 'slurm'
}

Nextflow's documentation describes how to set advanced configuration for HPCs.

tip

It's a good idea to submit the Nextflow process as a job