nf-core/configs: 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

conf/tuos_stanage
// 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
}
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