SGE cluster config for distiller

cluster.config

process{

    // SGE node config
    executor = 'sge'
    penv = 'sharedmem'
    clusterOptions = '-l h_vmem=4G -V'
    time='12h'
    cpus = 1
    maxRetries = 2
    distillerTmpDir='/exports/eddie/scratch/ifliamer'
    // errorStrategy = 'retry'

    withName: download_truncate_chunk_fastqs {        
        cpus = 4
        clusterOptions = '-l h_vmem=2G -V'
        time = { 2.hour * task.attempt }
    }

    withName: local_truncate_chunk_fastqs {        
        cpus = 4
        clusterOptions = '-l h_vmem=2G -V'
        time = { 2.hour * task.attempt }
    }

    withName: fastqc {
        cpus = 4
        clusterOptions = '-l h_vmem=4G -V'
        time = '2h'
    }

    withName: map_parse_sort_chunks {
        cpus = 4
        clusterOptions = '-l h_vmem=8G -V'
        time = { 2.hour * task.attempt }
    }


    withName: merge_dedup_splitbam {
        cpus = 4
        clusterOptions = '-l h_vmem=8G -V'
        time = { 12.hour * task.attempt }
    }

    withName: bin_zoom_library_pairs {
        cpus = 8
        clusterOptions = '-l h_vmem=8G -V'
        time = { 12.hour * task.attempt }
    }

    withName: merge_zoom_library_group_coolers {
        cpus = 4
        clusterOptions = '-l h_vmem=32G -V'
        time = { 12.hour * task.attempt }
    }


    //
    // $merge_stats_libraries_into_groups
    // { use defaults }
    //


}

singularity {
    enabled = false
    // mount external "/nearline" to internal "/mnt"
    runOptions = "--bind /nearline:/mnt:rw"
    // enable automount when available
    autoMounts = false
}


docker {
    enabled = false
}