Rosalind UGE Configuration
nf-core pipelines have been successfully configured for use on the Rosalind UGE cluster.
To use the Rosalind profile, run the pipeline with -profile rosalind_uge. This will download and apply ‘rosalind_uge.config’ which has been configured for the UGE cluster. This profile will allow all Nextflow processes to run within singularity containers, which will be downloaded and converted from docker containers, if needed.
Note: This profile does not configure resources but does partition jobs based on runtime to make use of
short.qandall.qnodes. If you require resources outside of the limits specified in the pipeline (ex. more memory, CPUS, or walltime), you will need to provide a custom config specifying needed resources.
Config file
/*
* ---------------------------------------------------------
* nf-core/configs: Rosalind UGE config
* ---------------------------------------------------------
*/
// Basic params of config file
params {
config_profile_description = 'Rosalind UGE config file'
config_profile_contact = 'Gregory Sprenger (@gregorysprenger)'
}
// Use Singularity
singularity {
enabled = true
autoMounts = true
}
// Submit up to 100 jobs at once with 15 secs between to avoid spamming the cluster
executor {
queueSize = 100
pollInterval = '15 sec'
}
// Process specific resource requirements
process {
// Error and retry handling
errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139, 71, 255] ? 'retry' : 'finish' }
maxRetries = 3
// Executor and queue information
executor = 'sge'
penv = 'smp'
queue = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
clusterOptions = { "-l h_vmem=${task.memory.toString().replaceAll(/[\sB]/, '')}" }
}
executor
sge
contact
