nf-core/configs: ipop_up
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iPOP-UP cluster profile, Université paris Cité

nf-core/configs: iPOP-UP Configuration

All nf-core pipelines have been successfully configured for use on the iPOP-UP cluster.

To use, run the pipeline with -profile ipop_up. This will download and launch the ipop_up.config which has been pre-configured with a setup suitable for the iPOP-UP cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.

Request an account

You will need an account to use iPOP-UP HPC cluster in order to run the pipeline, please refer to https://parisepigenetics.github.io/bibs/cluster/ipopup/.

Running the workflow on the iPOP-UP cluster

Guidelines to start nf-core workflows are provided at https://parisepigenetics.github.io/bibs/edctools/workflows/nf-cores.

In brief, Nextflow is installed on the iPOP-UP cluster and you need to activate it like this:

module load nextflow

Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. Nextflow shouldn’t run directly on the submission node but on a compute node. We recommand using a sbatch script:

nfcore-atac.sh

#!/bin/bash
#SBATCH --partition=ipop-up
#SBATCH --mem=4G
 
module purge
export JAVA_LD_LIBRARY_PATH=/shared/software/conda/envs/nextflow-21.04.0/lib/server
export JAVA_HOME=/shared/software/conda/envs/nextflow-21.04.0
module load nextflow/21.04.0
 
nextflow run nf-core/atacseq  -profile ipop_up -params-file nf-params.json

Launch on the cluster with sbatch:

sbatch nfcore-atac.sh

Test dataset

nf-core provides some test for each workflow:

#!/bin/bash
#SBATCH --partition=ipop-up
#SBATCH --mem=4G
 
module purge
export JAVA_LD_LIBRARY_PATH=/shared/software/conda/envs/nextflow-21.04.0/lib/server
export JAVA_HOME=/shared/software/conda/envs/nextflow-21.04.0
module load nextflow/21.04.0
 
nextflow run nf-core/atacseq  -profile ipop_up,test

Databanks

A local copy of several genomes are available in /shared/banks/ directory.

Config file

See config file on GitHub

conf/ipop_up

//Profile config names for nf-core/configs
params {
    config_profile_description = 'iPOP-UP cluster profile, Université paris Cité'
    config_profile_contact     = 'Magali Hennion, bibs@parisepigenetics.com'
    config_profile_url         = 'https://discourse.rpbs.univ-paris-diderot.fr/c/ipop-up'
}
 
singularity {
    // need one image per execution
    enabled    = true
    runOptions = '-B /shared'
}
 
process {
    resourceLimits = [
        memory: 100.GB,
        cpus: 28,
        time: 96.h
    ]
    executor = 'slurm'
    queue    = 'ipop-up'
}
 
params {
    igenomes_ignore = true
    // Max resources requested by a normal node on iPOP-UP cluster.
    max_memory      = 100.GB
    max_cpus        = 28
    max_time        = 96.h
}

nf-core/configs: ipop_up Edit