Workflows

Nextflow

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

. /local/env/envnextflow-20.10.0.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.

Alternatively, we provide some other pre-designed workflows for RNAseq and small-RNAseq analysis. They can be found in the directory /local/nextflow/ with the following pattern:

/local/nextflow/type_of_analysis/team_designer/

For more convenience, a shell wrapper is available for each workflow. You just have to copy it into your working directory, for example:

cp /local/nextflow/rnaseq/nfcore/rnaseq_nfcore.sh ~/workdir/

You may need to customize the script to suit your needs (data files, etc..), and run it with SLURM like this:

sbatch rnaseq_nfcore.sh

SnakeMake

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

. /local/env/envsnakemake-6.0.5.sh