parabricks-nextflow/nextflow.config at main · Elembio/parabricks-nextflow · GitHub

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// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

params {

    // input + output
    input                      = null
    outdir                     = './results'

    // Parabricks
    model_file                 = null
    target_region_bed          = null
    known_sites                = null
    proposed_variants          = null
    assay                      = "WGS"

    // References
    genome                      = null
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    igenomes_ignore            = false

    // samples
    ignore_samples             = ["Unassigned", "PhiX", "phiX", "CBPhiX", "Undetermined"]

    // nextflow
    publish_dir_mode           = 'copy'

    // sample batching
    batch_size                 = 12

    // Config options
    custom_config_version      = "main"
    custom_config_base         = "https://raw.githubusercontent.com/Elembio/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    max_multiqc_email_size     = '25.MB'
    multiqc_logo               = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '192.GB'
    max_cpus                   = 48
    max_time                   = '4.h'

}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

manifest {
    name            = 'parabricks/parabrick-nextflow'
    author          = 'Gary Burnett, Bryan R Lajoie, Carlos Ruiz Perez, Rosi Bajari, Max Mass'
    homePage        = 'https://github.com/clara-parabricks-workflows/parabricks-nextflow'
    description     = 'NVIDIA Parabricks WGS/WES workflow (fq2bam->deepvariant)'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=24.0.0'
    version         = '1.0.0'
}

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

    test { includeConfig 'conf/test.config' }
    test_small { includeConfig 'conf/test_small.config' }
    test_trinity_twist { includeConfig 'conf/test_trinity_twist.config' }
    test_trinity_idt { includeConfig 'conf/test_trinity_idt.config' }
    exome { includeConfig 'conf/exome.config' }
    genome { includeConfig 'conf/genome.config' }
    local { includeConfig 'conf/local.config' }
    ebc { includeConfig 'conf/ebc.config' }
}

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load custom config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load nf-core/sentieon-cli-nf custom profiles from different institutions.
try {
    includeConfig "${params.custom_config_base}/pipeline/parabricks_nextflow.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load pipeline config profile: ${params.custom_config_base}/pipeline/parabricks_nextflow.config")
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry   = 'quay.io'
docker.registry      = 'quay.io'
podman.registry      = 'quay.io'
singularity.registry = 'quay.io'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}

// Define check_max function
def check_max(value, resource_type) {
    // Replace this logic with your actual maximum limit checks
    def max_limit = (resource_type == 'cpus') ? 64 : (resource_type == 'memory' ? 128.GB : null)
    return value > max_limit ? max_limit : value
}