Novo Nordisk’s Einstein Configuration
Using the Einstein config profile
Before running any pipeline in Novo Nordisk’s Einstein cluster, Nextflow will need to be installed in the conda environment being used.
To use, run the pipeline with -profile einstein (one hyphen).
This will download and launch the einstein.config which has been pre-configured with a setup suitable for the Einstein server.
It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler.
Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) if needed before execution of the pipeline.
Below are non-mandatory information on e.g., required modules
Before running the pipeline you will need to have a working Nextflow installation and load Singularity using the environment module system on the Einstein cluster. You can do this by doing for example:
# Load Singularity environment modules
module load nextflow
module load singularityConfig file
/*
* ------------------------------------------------------------------
* Config file for nextflow pipelines for Novo Nordisk's Einstein cluster
* ------------------------------------------------------------------
*/
params {
config_profile_description = "Novo Nordisk's Einstein cluster profile"
config_profile_contact = 'Ashot Margaryan (ashotmarg2004@gmail.com)'
max_memory = "750.GB"
max_cpus = 64
max_time = "240.h"
}
process {
executor = 'slurm'
beforeScript = 'module purge; module load singularity/3.8.1'
scratch = true
maxRetries = 3
scratch = "/scratch/users/${USER}"
}
executor {
queueSize = 50
submitRateLimit = "10/1sec"
}
singularity {
enabled = true
autoMounts = true
cacheDir = "/scratch/users/${USER}"
}
