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.
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