roslin.config

//Profile config names for nf-core/configs
params {
    config_profile_description = 'University of Edinburgh (Eddie) cluster profile for Roslin Institute provided by nf-core/configs.'
    config_profile_contact = 'Sebastien Guizard (@sguizard) and Donald Dunbar (@ddunbar)'
    config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
}

executor {
    name = "sge"
}

process {
    stageInMode = 'symlink'
    scratch = 'false'
    penv = { task.cpus > 1 ? "sharedmem" : null }

    // To date (16/08/2024), the FastQC module is still broken.
    // More details here: https://github.com/nf-core/modules/pull/6156
    // Until the Pull Request is accepted, and the new version of the module is integrated to pipelines,
    // We force the amount of memory here.
    withName: 'FASTQC.*' {
        cpus = 5
        memory = '5.GB'
        // Check if an environment variable NFX_SGE_PROJECT exists, if yes, use the stored value for -P option
        // Otherwise set the project to uoe_baseline
        if (System.getenv('NFX_SGE_PROJECT')) {
            clusterOptions = {"-l rl9=false -l h=!node1d01 -l h_vmem=10G -pe sharedmem 5 -P $NFX_SGE_PROJECT"}
        } else {
            clusterOptions = {"-l rl9=false -l h=!node1d01 -l h_vmem=10G -pe sharedmem 5 -P uoe_baseline"}
        }
    }

    // This withName will override all jobs (except for FASTQC jobs, cf above) clusterOptions
    // This is necessary to allow jobs to run on Eddie for many users
    // For each job, we add an extra 4 Gb of memory.
    // For example, the process asked 16 Gb of RAM (task.memory). The job will reserve 20 Gb of RAM.
    // The process will still use 16 Gb (task.memory) leaving 4 Gb for other system processes.
    // This is very useful any JAVA programs which allocate task.memory RAM for its Virtual Machine
    // Also it leaves enough memory for singularity to unpack images.
    withName: '!.*FASTQC.*' {
        // Check if an environment variable NFX_SGE_PROJECT exists, if yes, use the stored value for -P option
        // Otherwise set the project to uoe_baseline
        if (System.getenv('NFX_SGE_PROJECT')) {
            clusterOptions = {"-l rl9=false -l h=!node1d01 -l h_vmem=${(task.memory + 8.GB).bytes/task.cpus} -P $NFX_SGE_PROJECT"}
        } else {
            clusterOptions = {"-l rl9=false -l h=!node1d01 -l h_vmem=${(task.memory + 8.GB).bytes/task.cpus} -P uoe_baseline"}
        }
    }

    // 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'
}

env {
    MALLOC_ARENA_MAX=1
}

singularity {
    envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
    runOptions = '-p -B "$TMPDIR"'
    enabled = true
    autoMounts = true
    cacheDir = '/exports/cmvm/eddie/eb/groups/alaw3_eb_singularity_cache'
}