CCGA Med Cluster Configuration
Deployment and testing of nf-core pipelines at the CCGA Med cluster is on-going.
To use, run the pipeline with -profile ccga_med. This will download and launch the ccga_med.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 load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
## Load Nextflow and Singularity environment modules
module purge
module load nextflow
module load singularity## Load Nextflow and Singularity environment modules
module purge
module load nextflow
module load singularityNB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner).
Config file
ccga_med.config
//Profile config names for nf-core/configs
params {
config_profile_description = 'CCGA Med 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 /work_ifs -B /scratch -B /work_beegfs"
cacheDir = "/work_beegfs/ikmb_repository/singularity_cache/"
}
executor {
queueSize=100
}
process {
// Global process config
executor = 'slurm'
queue = 'all'
}
params {
// illumina iGenomes reference file paths on RZCluster
igenomes_base = '/work_beegfs/ikmb_repository/references/iGenomes/references/'
saveReference = true
max_memory = 250.GB
max_cpus = 24
max_time = 120.h
}
ccga_med.config
//Profile config names for nf-core/configs
params {
config_profile_description = 'CCGA Med 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 /work_ifs -B /scratch -B /work_beegfs"
cacheDir = "/work_beegfs/ikmb_repository/singularity_cache/"
}
executor {
queueSize=100
}
process {
// Global process config
executor = 'slurm'
queue = 'all'
}
params {
// illumina iGenomes reference file paths on RZCluster
igenomes_base = '/work_beegfs/ikmb_repository/references/iGenomes/references/'
saveReference = true
max_memory = 250.GB
max_cpus = 24
max_time = 120.h
}
executor
slurm
contact
