Workflows

Nextflow

Nextflow is installed on the cluster, it can be used by sourcing the correct environnement:

. /local/env/envnextflow-23.04.1.sh

nf-core is also preinstalled, allowing you to use standard workflows from nf-co.re using the nf-core client.

Nextflow is preconfigured to use Singularity (when workflows are designed to use containers) and to distribute jobs on the Slurm cluster.

A GenOuest profile is available, to make sure the scratch, db, and groups folders are mounted in your singularity containers. You can select it by using the -profile genouest option.

SnakeMake

SnakeMake is pre-installed on the cluster, you can source it like that:

. /local/env/envsnakemake-7.28.3.sh