Leicester Configuration

All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester.

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

NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT. NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

Config file

See config file on GitHub

params {
  config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.'
  config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk'
  ACCOUNT = "cellfunc" // users, please set the bash variable DEFAULT_ACCOUNT or provide account to be used in analysis
  max_cpus = 24
  max_memory = 240.GB
  max_time = 168.h
singularity {
  enabled = true
  envWhitelist = 'TZ'
process {
  executor = 'slurm'
  cpus   = 1
  pollInterval = '1 min'
  queueStatInterval = '2 min'   
  memory =  24.GB
  time   = 12.h  
  withLabel: gpu {
      beforeScript = 'module load gcc/12.3.0 && module load cuda12.1/toolkit && module load cudnn8.9-cuda12.1'
      clusterOptions = { "--gres=gpu:ampere:1 --account="+params.ACCOUNT }
      containerOptions = {
            workflow.containerEngine == "singularity" ? '--containall --cleanenv --nv':
            ( workflow.containerEngine == "docker" ? '--gpus all': null )