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"
}
executor
contact
