Pôle Scientifique de Modélisation Numérique (PSMN)
All nf-core pipelines have been successfully configured for use on the tars cluster at the Institut Pasteur.
To use, run the pipeline with -profile psmn. This will download and launch the psmn.config which has been pre-configured with a setup suitable for the PSMN 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.
You can have more information on the cluster parition here: www.ens-lyon.fr/PSMN/Documentation/clusters_usage/computing_resources.html
Running the workflow on the PSMN cluster
Install Nextflow and Charliecloud
The Nextflow binary is available in the folder /Xnfs/abc/nextflow_bin/.
All the Charliecloud binaries are available in the folder /Xnfs/abc/charliecloud_bin/.
You can update your $PATH variable with the following command to have access to Nextflow and Charliecloud:
PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin/:$PATH
or add this line to your ~/.zshrc or ~/.bashrc configuration file.
Install nf-core
nf-core is available on the PSMN as a Charliecloud container you can run the classical nf-core command by prefixing them with:
ch-run -b /scratch:/scratch /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core
For exemple to download the nf-core/rnaseq pipeline you can use the command:
cd /Xnfs/abc/nf_scratch/<user_name>/
ch-run -b /scratch:/scratch -b /Xnfs:"" \
/Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
download rnaseq -r 3.9 --outdir nf-core-rnaseq
Download and launch a nf-core pipeline
You can use the nf-core download command to download an nf-core pipeline and the configuration files for the PSMN:
cd /Xnfs/abc/nf_scratch/<user_name>/
ch-run -b /scratch:/scratch \
/Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
download rnaseq -r 3.9 --outdir <your scratch directory>/nf-core-rnaseq -x none -c none
Download all the necessary image
By default the psmn profile will lookup charliecloud img in the /Xnfs/abc/charliecloud/ folder.
To download all the images that are not already present in this folder you can use the following script
cd nf-core-rnaseq
pull_ch_images_locally.sh
Launch the pipeline
Then you can launch this pipeline with the PSMN profile
tmux
cd nf-core-rnaseq
nextflow run workflow -profile test,psmn --outdir results/
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'PSMN (Pôle Scientifique de Modélisation Numérique) HPC cluster profile'
config_profile_contact = 'Laurent Modolo (@l-modolo)'
config_profile_url = 'http://www.ens-lyon.fr/PSMN/doku.php?id=en:accueil'
}
charliecloud {
enabled = true
cacheDir = "/Xnfs/abc/charliecloud"
runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
readOnlyInputs = true
}
process {
resourceLimits = [
memory: 370.GB,
cpus: 32,
time: 96.h
]
executor = 'slurm'
queue = "E5,Lake"
cpus = 1
memory = 32.GB
time = 24.h
withLabel: 'process_single|process_single_thread|sc_tiny|sc_small|sc_medium' {
queue = "Lake"
cpus = 1
memory = 96.GB
time = 24.h
}
withLabel: 'process_low|mc_small|process_very_low' {
queue = "Lake"
cpus = 16
memory = 80.GB
time = 24.h
}
withLabel: 'process_medium|mc_medium' {
queue = "Lake"
cpus = 32
memory = 180.GB
time = 48.h
}
withLabel: 'process_high|mc_large|mc_huge|process_high_cpus|cpus_max' {
queue = "Lake"
cpus = 32
memory = 370.GB
time = 48.h
}
withLabel: 'process_long|process_maximum_time|process_long_parallelized' {
queue = "Lake"
time = 96.h
}
withLabel: 'process_high_memory|memory_max' {
queue = "Epyc"
memory = 500.GB
}
withLabel: gpu {
queue = "E5-GPU"
}
}
params {
max_memory = 370.GB
max_cpus = 32
max_time = 96.h
}
executor
contact
