nextflow.config

def time_mod(time, attempt) {(attempt == 1) ? time : (time + (attempt * (time / 2)))}
def memory_mod(memory, attempt) {(attempt == 1) ? memory : (memory + (attempt * (memory / 2)))}

profiles {
    slurm {
        executor {
          $slurm {
            queueSize = 200
            pollInterval = '30 sec'
          }
           $local {
           cpus = 4
           memory = '8G'
           }      
        }
        process {
            executor = 'slurm'
            stageInMode = 'symlink'
            errorStrategy = 'retry'
            maxRetries = 1
            cache = 'lenient'
            
            withLabel: large {
                cpus = 16
                memory = { memory_mod(96.GB, 1) } 
                time = { time_mod(4.hour, 1) }
                queue = 'genomics'
                clusterOptions = '--account=ls25 --qos=genomics'    
            }
            withLabel: big {
                cpus = 4
                memory = { memory_mod(16.GB, 1) } 
                time = { time_mod(4.hour, 1) }
                queue = 'genomics'
                clusterOptions = '--account=ls25 --qos=genomics'    
            }
        }
    }
}


manifest {
    homePage = 'https://github.com/alexyfyf/atac_nf'
    description = 'ATAC-seq analysis Nextflow pipeline'
    version = '7f996b7'
    mainScript = 'atac.nf'
    author = 'Feng.Yan@monash.edu'
}