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`](../conf/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.
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](http://abims.sb-roscoff.fr/account).
## Running the workflow on the ABiMS cluster
Nextflow is installed on the ABiMS cluster. Some documentation is available on the [ABiMS website](http://abims.sb-roscoff.fr/resources/cluster/howto#nextflow).
You need to activate it like this:
```bash
module load nextflow/20.04.1 slurm-drmaa/1.0.8
```
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:
```bash
# Login to a compute node
srun --pty bash
# Load the dependencies if not done before
module load nextflow/20.04.1 slurm-drmaa/1.0.8
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
/path/to/nf-core/workflow \\
-resume
-profile abims \\
--email my-email@example.org \\
-c my-specific.config
...
# Or use the nf-core client
nextflow run nf-core/rnaseq ...
```
## Databanks
A local copy of several genomes are available in `/shared/bank` directory.
