mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-04 20:49:54 +00:00
15 lines
1.1 KiB
Markdown
15 lines
1.1 KiB
Markdown
# 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.
|