nf-core/configs: pe2
New York Genome Center (NYGC) cluster profile provided by nf-core/configs.
New York Genome Center Configuration
To use, run a pipeline with -profile pe2. This will download and launch the pe2.config which has been
pre-configured with a setup suitable for the PE2 cluster (NYGC legacy). Using this profile, container images with all required software will be pulled before execution of a job requiring that software.
Module Requirements
In order to run a pipeline on the NYGC cluster, you will need to load the following modules:
module load singularity/3.8.6
module load nextflow/22.10.4Note: All of the intermediate files generated from running a pipeline will be stored in the work/ subdirectory of where the pipeline was launched. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the defined output directory as well.
Config file
singularityDir = "${HOME}/.singularity/singularity_images_nextflow"
singularity {
enabled = true
autoMounts = true
cacheDir = singularityDir
}
process {
executor = 'slurm'
queue = { task.accelerator ? 'gpu' : (task.memory > 100.GB ? 'bigmem' : 'pe2') }
}
params {
config_profile_contact = 'John Zinno (@jzinno)'
config_profile_description = 'New York Genome Center (NYGC) cluster profile provided by nf-core/configs.'
config_profile_url = 'https://www.nygenome.org/'
}
executor {
queueSize = 196
submitRateLimit = '5 sec'
}
executor
contact
