mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 00:26:03 +00:00
18 lines
1.2 KiB
Markdown
18 lines
1.2 KiB
Markdown
# nf-core/configs: FGCZ Configuration
|
|
|
|
Configuration file to run nf-core pipelines on the cluster of the [Functional Genomics Center Zurich](https://fgcz.ch/), a research and training facility of the ETH Zürich and the University of Zurich.
|
|
|
|
Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines.
|
|
|
|
To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.
|
|
The config places the singularity cache in your /srv/GT/ directory for access by all projects.
|
|
|
|
Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz
|
|
|
|
## Before running the pipeline
|
|
|
|
Load the following modules before running any nf-core pipelines.
|
|
|
|
```bash
|
|
module load Dev/Python/3.8.3
|
|
```
|