nf-configs/docs/sbc_sharc.md

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:

• nf-co.re/atacseq
• nf-co.re/chipseq
• nf-co.re/rnaseq
• nf-co.re/sarek

When using sbc_sharc.config with the pipelines listed above, the appropriate configuration file from the list below will be loaded automatically:

• atacseq sbc_sharc.config
• chipseq sbc_sharc.config
• rnaseq sbc_sharc.config
• sarek sbc_sharc.config

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