nextflow.config

/*
* This configuration file is main one. This includes the pipeline parameters
* and different config files, one for each profile.
* You can switch among them using the Nextflow parameter -profile <<PROFILENAME>>
*/


// include the pipeline parameters from this file
includeConfig "$projectDir/params.config"

params {

    // Boilerplate options    
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    help                       = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes'
    enable_conda               = false

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '10.GB'
    max_cpus                   = 8
    max_time                   = '240.h'

}


// this should help in removing the "work" directory after the processes have finished successfully if true
cleanup = false


// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

profiles {
    docker {
        conda.enabled          = false
        docker.enabled         = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
}

manifest {
    name            = 'selenoprofiles-nf'
    author          = 'Emilio Righi'
    homePage        = 'https://github.com/guigolab/selenoprofiles-nf'
    description     = 'Seleno Profiles annotation of eukaryotic genomes'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '0.1'
}