CCGA DX Configuration
Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going.
To use, run the pipeline with -profile ccga_dx. This will download and launch the ccga_dx.config which has been pre-configured with a setup suitable for the CCGA 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.
Before running the pipeline you will need to have Nextflow installed.
NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'CCGA DX cluster profile provided by nf-core/configs.'
config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
config_profile_url = 'https://www.ccga.uni-kiel.de/'
}
/*
* -------------------------------------------------
* Nextflow config file for CCGA cluster in Kiel
* -------------------------------------------------
*/
singularity {
enabled = true
runOptions = "-B /mnt -B /work_ifs"
}
executor {
queueSize = 100
}
process {
resourceLimits = [
memory: 250.GB,
cpus: 20,
time: 240.h
]
// Global process config
executor = 'slurm'
queue = 'htc'
}
params {
// illumina iGenomes reference file paths on DX Cluster
igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
saveReference = true
max_memory = 250.GB
max_cpus = 20
max_time = 240.h
}
executor
slurm
contact
