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

//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 {  
  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  
}