nextflow.config

// Define executors options
executor {
    $slurm {
        queueSize = 40
    }

    $local {
        cpus = 4
        queueSize = 1
    }
}

profiles {

    standard {
        
        conda.enabled = true
        conda.useMamba = true

        process {
            executor = 'local'
            cpus = 4
            conda = 'conda_envs/general_env.yml'
        }

    }

    cluster {

        conda.enabled = true
        conda.useMamba = true
        conda.createTimeout = '50 min'
        
        process {
            
            conda = 'conda_envs/general_env.yml'

            executor = 'slurm'
            
            withLabel: 'q1d' {
                time = '23:59:00'
                cpus = 8
                memory = '16G'
                clusterOptions = '--qos=1day'
            }

            withLabel: 'q6h' {
                time = '06:00:00'
                cpus = 8
                memory = '16G'
                clusterOptions = '--qos=6hours'
            }

            withLabel: 'q30m' {
                time = '00:30:00'
                cpus = 8
                memory = '16G'
                clusterOptions = '--qos=30min'
            }

            withLabel: 'q6h_16cores' {
                time = '05:58:00'
                cpus = 16
                memory = '32G'
                clusterOptions = '--qos=6hours'
            }

            withLabel: 'q30m_1core' {
                time = '00:30:00'
                cpus = 1
                memory = '16G'
                clusterOptions = '--qos=30min'
            }
            
            withLabel: 'q30m_highmem' {
                time = '00:30:00'
                cpus = 8
                memory = '32G'
                clusterOptions = '--qos=30min'
            }
            
            withLabel: 'q6h_subsample' {
                time = '02:00:00'
                cpus = 16
                memory = '32G'
                clusterOptions = '--qos=6hours'
            }

            withLabel: 'q6h_2h' {
                time = '02:00:00'
                cpus = 8
                memory = '16G'
                clusterOptions = '--qos=6hours'
            }

            withLabel: 'medaka_setup' {
                executor = 'local'
                conda = 'conda_envs/medaka_env.yml'
            }

        }
        
    }

}

// generate report of the run
report {
    enabled = true
    file = 'report.html'
    overwrite = true
}