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15 lines
1.1 KiB
Markdown
15 lines
1.1 KiB
Markdown
# nf-core/configs: Cancer Research UK Manchester Institute Configuration
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All nf-core pipelines have been successfully configured for the use on the HPC (phoenix) at Cancer Research UK Manchester Institute.
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To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/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.
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Before running the pipeline you will need to load Nextflow using the environment module system, for example via:
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```bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load apps/nextflow/22.04.5
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```
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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.
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