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 singularity

Config file

See config file on GitHub

* ------------------------------------------------------------------
*   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 ('
    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}"