All nf-core pipelines have been successfully configured for use on the BioHPC Genomics (biohpc_gen) cluster that is housed at the Leibniz Rechenzentrum (LRZ) for research groups at the Faculty of Biology of the Ludwig-Maximilians-University (LMU) in Munich.
To use, run the pipeline with -profile biohpc_gen. This will download and launch the biohpc_gen.config which has been pre-configured with a setup suitable for the biohpc_gen cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Charliecloud container before execution of the pipeline.
NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines.
To correctly submit jobs into the biohpc_gen cluster the SLURM_CLUSTERS variable needs to be set:
export SLURM_CLUSTERS=biohpc_genRecent versions can be installed via spack and made available as a module.
Cluster specific instructions to load spack:
module load spack
module load user_spackWe recommend to use charliecloud >= 0.35.
spack install [email protected]
spack module tcl refresh charliecloud
module avail charliecloudIn addition we recommend using nextflow >= 24.04.2. This can be installed via spack:
spack install [email protected]
spack module tcl refresh nextflow
module avail nextflowThese are then available as modules (please confirm the module name using module avail)
## Load Nextflow and Charliecloud environment modules
module load nextflow/24.04.2-gcc12 charliecloud/0.35-gcc12NB: bioHPC compute nodes are submit hosts. This means you can submit the nextflow head job via sbatch.
NB: Sometimes you may want to have jobs submitted 'locally' in a large nextflow job. Details on this can be found here https://doku.lrz.de/nextflow-on-hpc-systems-test-operation-788693597.html