tuos_stanage.md

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