Sheffield Bioinformatics Core Facility Stanage Configuration

Using the tuos_stanage Institutional Configuration Profile

To use tuos_stanage.config, run nextflow with an nf-core pipeline using -profile tuos_stanage (note the single hyphen).

This will download and launch tuos_stanage.config which has been pre-configured with a setup suitable for the Stanage cluster and will automatically load the appropriate pipeline-specific configuration file.

A Note on Singularity Containers

The tuos_stanage.config configuration file supports running nf-core pipelines with Singularity containers; Singularity images will be downloaded automatically before execution of the pipeline.

When you run nextflow for the first time, Singularity will create a hidden directory .singularity in your $HOME directory /users/$USER which has limited (75GB) space available. It may therefore a good idea to create a directory somewhere else (e.g., /mnt/parscratch/users/$USER) with more room and link the locations. To do this, run the following series of commands:

# change directory to $HOME
cd $HOME
 
# make the directory that will be linked to
mkdir /mnt/parscratch/users/$USER/.singularity
 
# link the new directory with the existing one
ln -s /mnt/parscratch/users/$USER/.singularity .singularity

Config file

See config file on GitHub

tuos_stanage.config
// Sheffield Bioinformatics Core Configuration Profile - Stanage
// Base Institutional Configuration
 
 
// nf-core specific parameters displayed in header summary of each run
 
params {
 
  config_profile_description = 'Sheffield Bioinformatics Core - Stanage'
  config_profile_contact = 'Sheffield Bioinformatics Core (bioinformatics-core@sheffield.ac.uk)'
  config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/stanage/index.html#stanage'
 
}
 
 
// hpc resource limits
 
params {
  
  max_cpus = 64
  max_memory = 251.GB
  max_time = 96.h
 
}
 
 
// hpc configuration
 
process {
 
  // scheduler
 
  executor = 'slurm'
 
}
 
 
// optional executor settings
 
executor {
 
  queueSize = 50
  submitRateLimit = '1 sec'
 
}
 
 
// container engine
 
singularity {
 
  enabled = true
  autoMounts = true
 
}