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nf-configs/docs/crukmi.md
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nf-core/configs: Cancer Research UK Manchester Institute Configuration

All nf-core pipelines have been successfully configured for the use on the HPC (phoenix) at Cancer Research UK Manchester Institute.

To use, run the pipeline with -profile crukmi. This will download and launch the crukmi.config which has been pre-configured with a setup suitable for the phoenix HPC. Using this profile, singularity images will be downloaded to run on the cluster.

Before running the pipeline you will need to load Nextflow using the environment module system, for example via:

## Load Nextflow and Singularity environment modules
module purge
module load apps/nextflow/22.04.5

The pipeline should always be executed inside a workspace on the /scratch/ system. All of the intermediate files required to run the pipeline will be stored in the work/ directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the results/ directory.