Nextflow is installed on the cluster, it can be used by sourcing the correct environnement:
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:
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:
SnakeMake is pre-installed on the cluster, you can source it like that: