mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 00:26:03 +00:00
32 lines
1.3 KiB
Markdown
32 lines
1.3 KiB
Markdown
# 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
|
|
# alternative module load jdk/1.8.0_291 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
|
|
```
|