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
// 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 {
resourceLimits = [
memory: 251.GB,
cpus: 64,
time: 96.h
]
// scheduler
executor = 'slurm'
}
// optional executor settings
executor {
queueSize = 50
submitRateLimit = '1 sec'
}
// container engine
singularity {
enabled = true
autoMounts = true
}
executor
contact
