eddie.config

//Profile config names for nf-core/configs
params {
    config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.'
    config_profile_contact     = 'Graeme Grimes (@ggrimes)'
    config_profile_url         = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
}

executor {
    name = "sge"
}

process {
    resourceLimits = [
        memory: 384.GB,
        cpus: 32,
        time: 240.h
    ]
    clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes / task.cpus}" : null }
    stageInMode    = 'symlink'
    scratch        = 'false'
    penv           = { task.cpus > 1 ? "sharedmem" : null }

    // common SGE error statuses
    errorStrategy  = { task.exitStatus in [143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
    maxErrors      = '-1'
    maxRetries     = 3

    beforeScript   = '''
    . /etc/profile.d/modules.sh
    module load singularity
    export SINGULARITY_TMPDIR="$TMPDIR"
    '''
}

params {
    // iGenomes reference base
    igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
    max_memory    = 384.GB
    max_cpus      = 32
    max_time      = 240.h
}

env {
    MALLOC_ARENA_MAX = 1
}

singularity {
    envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
    runOptions   = '-p -B "$TMPDIR"'
    enabled      = true
    autoMounts   = true
    cacheDir     = "/exports/igmm/eddie/BioinformaticsResources/nfcore/singularity-images"
}