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 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.
module load Dev/Python/3.8.3Config file
params {
config_profile_description = "FGCZ ETH/UZH"
config_profile_contact = "natalia.zajac@fgcz.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 = 30
}
singularity {
enabled = true
autoMounts = true
cacheDir = "/srv/GT/nextflow/singularity/"
}
executor
contact
