mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 00:26:03 +00:00
35 lines
1.9 KiB
Markdown
35 lines
1.9 KiB
Markdown
# nf-core/configs: University of Ghent High Performance Computing Infrastructure (VSC)
|
|
|
|
> **NB:** You will need an [account](https://www.ugent.be/hpc/en/access/faq/access) to use the HPC cluster to run the pipeline.
|
|
|
|
First you should go to the cluster you want to run the pipeline on. You can check what clusters have the most free space on this [link](https://shieldon.ugent.be:8083/pbsmon-web-users/). Use the following commands to easily switch between clusters:
|
|
|
|
```shell
|
|
module purge
|
|
module swap cluster/<CLUSTER>
|
|
```
|
|
|
|
Before running the pipeline you will need to create a PBS script to submit as a job.
|
|
|
|
```bash
|
|
#!/bin/bash
|
|
|
|
module load Nextflow
|
|
|
|
nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
|
|
```
|
|
|
|
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 anyway.
|
|
The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration
|
|
|
|
You can also add several TORQUE options to the PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B).
|
|
|
|
To submit your job to the cluster by using the following command:
|
|
|
|
```shell
|
|
qsub <script name>.pbs
|
|
```
|
|
|
|
> **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`.
|
|
|
|
> **NB:** The default directory where the `work/` and `singularity/` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.
|