nf-core/configs: ilifu
Ilifu (https://ilifu.ac.za) slurm cluster profile provided by nf-core/configs.Ilifu slurm cluster configuration
To use, run the pipeline with -profile ilifu. This will use the ilifu.config which has been pre-configured
with a setup suitable for the Ilifu slurm cluster. In particular it configures the use of Singularity containers and chooses an
appropriate queue based on the memory required and the need (or lack of need) for a GPU (as specified using the
accelerator attribute of the Nextflow process).
Running the workflow on the Ilifu slurm cluster
Mextflow is made available using the Environment Modules system. Load the Nextflow module with module load nextflow.
Do not run Nextflow directly on the login node, rather write a script that executes module load nextflow and then
runs the workflow with nextflow -profile ilifu.
Singularity containers are cached in the directory specified by NXF_SINGULARITY_CACHEDIR. Ensure that this directory exists and
that the environment variable is set to ensure that you re-use Singularity container images.
An example script illustrating the execution of a (fictional) workflow follows:
#!/bin/bash
#SBATCH -J my_pipeline
NXF_SINGULARITY_CACHEDIR=/projects/bio/sanbi/singularity_images
export NXF_SINGULARITY_CACHEDIR
module add nextflow
nextflow run nf-core/my_pipeline -profile ilifu \
-w /path/to/some/dir/work \
-resume
--some_parameter
## clean up on exit 0 - delete this if you want to keep the work dir
status=$?
if [[ $status -eq 0 ]]; then
rm -r /path/to/some/dir/work
fi
Memory, CPU and time limits can be imposed by providing --max_memory, --max_cpus and --max_time paramaters to the workflow run.
To check which versions of Nextflow are installed on the cluster and which is the default version, use the module avail nextflow command. If a
newer version is required, contact Ilifu support.
Config file
params {
config_profile_description = """
Ilifu (https://ilifu.ac.za) slurm cluster profile provided by nf-core/configs.
""".stripIndent()
config_profile_contact = 'Peter van Heusden (@pvanheus)'
config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/ilifu.md'
max_memory = 1500.GB
max_cpus = 96
max_time = 336.h
}
singularity {
enabled = true
autoMounts = true
}
process {
resourceLimits = [
memory: 1500.GB,
cpus: 96,
time: 336.h
]
beforeScript = """
module load singularity
""".stripIndent()
executor = 'slurm'
queue = { task.accelerator != null && task.accelerator.contains('nvidia') ? 'GPU' : (task.memory >= 250.GB ? 'HighMem' : 'Main') }
}
executor
contact
