IFB core Configuration
All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique).
To use, run the pipeline with -profile ifb_core. This will download and launch the ifb_core.config which has been pre-configured with a setup suitable for the IFB core 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.
How to use on IFB core
Here is the link to the cluster’s documentation. Before running the pipeline you will need to load Nextflow and other dependencies using the environment module system on IFB core. You can do this by issuing the commands below:
# Login to a compute node
srun --pty bash
## Load Nextflow and Singularity environment modules
module purge
module load nextflow
module load singularity
module load openjdk
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
nf-core/workflow \\
-resume
-profile ifb_core \\
--email my-email@example.org \\
-c my-specific.config
...
# Or use the nf-core client
nextflow run nf-core/rnaseq ...
Databanks
A local copy of several genomes are available in /shared/bank directory. See
our databank page
to search for your favorite genome.
NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to account page.
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'The IFB core cluster profile'
config_profile_contact = 'https://community.france-bioinformatique.fr'
config_profile_url = 'https://ifb-elixirfr.gitlab.io/cluster/doc/cluster-desc/'
}
singularity {
enabled = true
runOptions = '-B /shared'
}
process {
resourceLimits = [
memory: 252.GB,
cpus: 56,
time: 720.h
]
executor = 'slurm'
queue = { task.time <= 24.h ? 'fast' : 'long' }
}
params {
igenomes_ignore = true
max_memory = 252.GB
max_cpus = 56
max_time = 720.h
}
executor
contact
