abims.md

nf-core/configs: ABiMS Configuration

All nf-core pipelines have been successfully configured for use on the ABiMS cluster.

To use, run the pipeline with -profile abims. This will download and launch the abims.config which has been pre-configured with a setup suitable for the ABiMS 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.

Request an account

You will need an account to use the HPC cluster on ABiMS in order to run the pipeline. If in doubt see http://abims.sb-roscoff.fr/account.

Running the workflow on the ABiMS cluster

Nextflow is installed on the ABiMS cluster.

You need to activate it like this:

module load nextflow slurm-drmaa graphviz

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. Run nextflow from a compute node:

# Load the dependencies if not done before
module load nextflow slurm-drmaa graphviz

# Run a downloaded/git-cloned nextflow workflow from
srun nextflow run \
/path/to/nf-core/workflow \
-profile abims \
--email my-email@example.org  \
-c my-specific.config
...

# Or use let nf-core client download the workflow
srun nextflow run nf-core/rnaseq -profile abims ...

# To launch in background
sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..."

Or write a sbatch script

nfcore-rnaseq.sh

#!/bin/bash
#SBATCH -p fast
#SBATCH --mem=4G

module load nextflow slurm-drmaa graphviz
nextflow run nf-core/rnaseq -profile abims ...

Launch on the cluster with sbatch:

sbatch nfcore-rnaseq.sh

Hello, world

nf-core provides some test for each workflow:

module load nextflow slurm-drmaa graphviz
nextflow run nf-core/rnaseq -profile abims,test

Singularity images mutualized directory

To reduce the disk usage, nf-core images can be stored in a mutualized directory: /shared/software/singularity/images/nf-core/

The environment variable NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow will indicate this directory to nextflow.

Databanks

A local copy of several genomes are available in /shared/bank/ directory.