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.q and all.q nodes. 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

See config file on GitHub

rosalind_uge.config
/*
* ---------------------------------------------------------
*       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]/, '')}" }
}