ABiMS Configuration

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

To use, run the pipeline with -profile abims. This will download and launch the abims.config which has been pre-configured with a setup suitable for the ABiMS cluster.

Request an account

You will need an account to use the HPC cluster on ABiMS in order to run the pipeline. If in doubt see https://my.sb-roscoff.fr.

Running the workflow on the ABiMS cluster

Nextflow is installed on the ABiMS cluster.

Launch it using srun

You need to activate it like this:

module load nextflow slurm-drmaa graphviz

Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command in background. Even if the job won’t run directly on the login node, please launch Nextflow on a compute node:

# Load the dependencies if not done before
module load nextflow slurm-drmaa graphviz
# Run Nextflow, it will submit the jobs with the resources needed on the cluster
srun nextflow run nf-core/rnaseq -r 3.10.1 -profile abims ...
# To launch in background
sbatch --wrap "nextflow run nf-core/rnaseq -r 3.10.1 -profile abims ..."

Or write a sbatch script


#SBATCH -p fast
#SBATCH --mem=4G
module load nextflow slurm-drmaa graphviz
nextflow run nf-core/rnaseq -r 3.10.1 -profile abims ...

Launch on the cluster with sbatch:

sbatch nfcore-rnaseq.sh

Hello, world

nf-core provides some test for each workflow:

module load nextflow slurm-drmaa graphviz
srun nextflow run nf-core/rnaseq -r 3.10.1 -profile abims,test

Singularity images mutualized directory

To reduce the disk usage, nf-core images can be stored in a mutualized directory: /shared/software/singularity/images/nf-core/

The abims profil includes the dedicade environment variable NXF_SINGULARITY_CACHEDIR to indicate the cache directory to nextflow.

If you need more images, please contact the support team


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

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'The ABiMS cluster profile'
    config_profile_contact = 'Gildas Le Corguillé (@lecorguille)'
    config_profile_url = 'https://abims.sb-roscoff.fr'
singularity {
    enabled = true
    autoMounts = true
    runOptions = '-B /shared:/shared'
    cacheDir = "/shared/software/singularity/images/nf-core/"
process {
    executor = 'slurm'
    queue    = { task.memory <= 250.GB ? (task.time <= 24.h ? 'fast' : 'long') : 'bigmem' }
params {
    igenomes_ignore = true
    max_memory = 750.GB
    max_cpus = 200
    max_time = 30.d