nf-core/configs: fgcz
FGCZ ETH/UZH
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 and nf-core/atacseq, 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 an apptainer image before execution of the pipeline. This requires a local installation of apptainer. 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 apptainer cache in your /srv/GT/software/apptainer/cache directory for access by all projects.
For example:
nextflow run -profile fgcz ...
Before running the pipeline
You may need to load the jdk module before running any nextflow pipelines.
module load Dev/jdk/21
Config file
params { config_profile_description = "FGCZ ETH/UZH" config_profile_contact = "falnoe@ethz.ch" max_memory = 500.GB max_cpus = 64 max_time = 240.h}
process { resourceLimits = [ memory: 500.GB, cpus: 64, time: 240.h ] executor = "slurm" maxRetries = 2}
executor { queueSize = 10}
apptainer { enabled = true autoMounts = true cacheDir = "/srv/GT/software/apptainer/cache"}