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nf-core/configs: 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/