mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-25 01:19:54 +00:00
35 lines
1.7 KiB
Markdown
35 lines
1.7 KiB
Markdown
# nf-core/configs: ku_sund_dangpu 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 java/11.0.15 nextflow/22.04.4 singularity/3.8.0
|
|
# alternative modules for older nextflow version (v.21) that works with java 8:
|
|
# module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0
|
|
export NXF_OPTS='-Xms1g -Xmx4g'
|
|
export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
|
|
export NXF_TEMP=/scratch/tmp
|
|
export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
|
|
```
|
|
|
|
Create the user-specific nextflow directories if they don't exist yet:
|
|
|
|
```
|
|
mkdir $NXF_SINGULARITY_CACHEDIR
|
|
mkdir $NXF_HOME
|
|
```
|
|
|
|
Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
|
|
|
|
```
|
|
nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
|
|
```
|