nf-configs/docs/fgcz.md

nf-core/configs: FGCZ Configuration

Configuration file to run nf-core pipelines on the cluster of the Functional Genomics Center Zurich, 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 your singularity cashe in your home directory for access by other projects your run in other working directories.

Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz

Before running the pipeline

Load the following modules before running any nf-core pipelines.

module load Dev/Python/3.8.3