2.4 KiB
nf-core/configs: Sheffield Bioinformatics Core Facility ShARC Configuration
Using the SBC_ShARC Institutional Configuration Profile
To use sbc_sharc.config, run nextflow with an nf-core pipeline using -profile sbc_sharc (note the single hyphen).
This will download and launch sbc_sharc.config which has been pre-configured with a setup suitable for the ShARC cluster and will automatically load the appropriate pipeline-specific configuration file.
The following nf-core pipelines have been successfully configured for use on the the University of Sheffield ShARC cluster:
When using sbc_sharc.config with the pipelines listed above, the appropriate configuration file from the list below will be loaded automatically:
The sbc_sharc.config configuration file might work with other nf-core pipelines as it stands but we cannot guarantee they will run without issue. We will be continuing to create, test and optimise configurations for new pipelines in the future.
A Note on Singularity Containers
The sbc_sharc.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 $HOME directory /home/$USER which has very very limited (10GB) space available. It is therefore a good idea to create a directory somewhere else (e.g., /data/$USER) with more room and link the locations. To do this, run the following series of commands:
# change directory to $HOME
cd $HOME
# make the directory that will be linked to
mkdir /data/$USER/.singularity
# link the new directory with the existing one
ln -s /data/$USER/.singularity .singularity