nf-configs/docs/ku_sund_dangpu.md

# nf-core/configs: PROFILE Configuration

All nf-core pipelines have been successfully configured for use on the DANGPU at the 
Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen.

To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU.

## Modules

Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. You can do this by issuing the commands below:

```bash
## Load Nextflow and Singularity environment modules
module purge
module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 
export NXF_OPTS='-Xms1g -Xmx4g'
export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
export NXF_TEMP=/scratch/tmp
NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images 
```

create nextflow directories if they dont exist:
```
mkdir $NXF_SINGULARITY_CACHEDIR
mkdir $NXF_HOME
```

finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` 
```
nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
```