The University of York Viking profile
York University Viking Configuration
This config is for running nf-core pipelines, either directly on Viking or via tower.nf
To use, run the pipeline with
-profile york_viking. This will download and launch the
york_viking.config which has been pre-configured with a setup suitable for the Viking cluster.
I recommend running Nextflow via tower.nf, in which case make sure to include the york_viking profile within the pipeline.
However, should you need to run it directly on the HPC follow the guidance below.
Loading the required modules
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the Viking cluster. You can do this by issuing the commands below:
You may want to add those module load commands to your shell configuration file if you use them often.
You need to make sure that the following environmental variables are set (pointing to appropriate dirs):
Running the nextflow pipeline
Create a params.json file with the desired parameters for the pipeline. Place this file in the folder from which you wish to run the Nextflow pipeline. Then using a screen session: