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-ebi)"
    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" // to avoid fail when using storeDir for missing output
}

executor {
    name = "lsf"
    queueSize = 2000
    submitRateLimit = "10/1sec"
    exitReadTimeout = "30 min"
    jobName = {
        task.name // [] and " " not allowed in lsf job names
            .replace("[", "(")
            .replace("]", ")")
            .replace(" ", "_")
    }
}