Sheffield Bioinformatics Core - Stanage
Sheffield Bioinformatics Core Facility Stanage Configuration
Using the tuos_stanage Institutional Configuration Profile
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
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
/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: