nf-configs/docs/crukmi.md

# 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`](../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.

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

```bash
## 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.
Written a help file 2022-08-12 15:57:04 +00:00			`# nf-core/configs: Cancer Research UK Manchester Institute Configuration`
Initial attempt at a CRUKMI config file 2022-08-12 14:43:22 +00:00
Written a help file 2022-08-12 15:57:04 +00:00			`All nf-core pipelines have been successfully configured for the use on the HPC (phoenix) at Cancer Research UK Manchester Institute.`
Initial attempt at a CRUKMI config file 2022-08-12 14:43:22 +00:00
Written a help file 2022-08-12 15:57:04 +00:00			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.
Initial attempt at a CRUKMI config file 2022-08-12 14:43:22 +00:00
Written a help file 2022-08-12 15:57:04 +00:00			`Before running the pipeline you will need to load Nextflow using the environment module system, for example via:`
Initial attempt at a CRUKMI config file 2022-08-12 14:43:22 +00:00
Written a help file 2022-08-12 15:57:04 +00:00			```bash
			`## Load Nextflow and Singularity environment modules`
			`module purge`
			`module load apps/nextflow/22.04.5`
			```

Ran prettier 2022-08-15 08:33:30 +00:00			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.