ebi_codon.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for EMBL-EBI Codon Cluster
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Author: Saul Pierotti
Mail: saul@ebi.ac.uk
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params {
    config_profile_contact     = "Saul Pierotti (@saulpierotti)"
    config_profile_description = "The European Bioinformatics Institute HPC cluster (codon) profile"
    config_profile_url         = "https://www.ebi.ac.uk/"
}

singularity {
    enabled     = true
    // the default is 20 minutes and fails with large images
    pullTimeout = "3 hours"
}

process {
    queue         = {
        if (task.time > 7.day && task.memory > 300.GB) {
            "long_bigmem"
        }
        else if (task.memory > 300.GB) {
            "bigmem"
        }
        else if (task.time > 7.day) {
            "long"
        }
        else if (task.time > 1.day) {
            "research"
        }
        else {
            "short"
        }
    }
    // this is to avoid errors for missing files due to shared filesystem latency
    maxRetries    = 3
    errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" }
    cache         = "lenient"
    afterScript   = "sleep 60"
}

executor {
    name            = "lsf"
    queueSize       = 2000
    submitRateLimit = "10/1sec"
    exitReadTimeout = "30 min"
    jobName         = {
        task.name
            .replace("[", "(")
            .replace("]", ")")
            .replace(" ", "_")
    }
}