Institut Pasteur Configuration

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 pasteur. This will download and launch the pasteur.config which has been pre-configured with a setup suitable for the Pasteur 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.

Running the workflow on the Pasteur cluster

Nextflow is not installed by default on the Pasteur cluster.

  • Install Nextflow : here

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. The compute nodes don’t have access to internet so you need to run it offline.

To do that:

  1. Create a virtualenv to install nf-core
module purge
module load Python/3.6.0
module load java
module load singularity
cd /path/to/nf-core/workflows
virtualenv .venv -p python3
. .venv/bin/activate
  1. Install nf-core: here
  2. Get nf-core pipeline and container: here
  3. Get the nf-core Pasteur profile: here
  4. Run nextflow on a compute node:
# create a terminal
# Get a compute node
# Load the dependencies if not done before
module purge
module load java
module load singularity
# Run nextflow workflow
nextflow run \\
/path/to/pipeline-dir/from/step/3/workflow \\
-profile pasteur \\
-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
--email  \\
--custom_config_base /path/to/configs/from/step/4/ \\
-c my-specific.config

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'The Institut Pasteur HPC cluster profile'
    config_profile_contact = 'Remi Planel (@rplanel)'
    config_profile_url = ''
singularity {
    enabled = true
    autoMounts = true
    runOptions = '-B /local/scratch:/tmp'
process {
    executor = 'slurm'
params {
    igenomes_ignore = true
    igenomesIgnore = true //deprecated
    max_memory = 256.GB
    max_cpus = 28
    max_time = 24.h