nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    yavsap Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {
     // Input options
    input = '.'
    platform = null
    paired = (params.platform == 'illumina')
    interleaved = false
    seed = 42

    // Reference genome options
    genome = 'NC_001437.1' // JEV RefSeq
    genome_list = 'jev'

    // Kraken 2 options
    kraken2_db = null
    keep_taxid = '0 10239' // 0 = Unclassified, 10239 = Viral

    // Read trimming options (shared)
    trim_minlen = 100
    trim_headcrop = 0

    // Illumina trimming options (Trimmomatic)
    trim_adapters = 'NexteraPE-PE.fa'
    trim_mismatches = 2
    trim_pclip = 30
    trim_clip = 10
    trim_winsize = 50
    trim_winqual = 15
    trim_leading = 15
    trim_trailing = 15
    trim_crop = 0

    // ONT-specific trimming options (Filtlong)
    trim_maxlen = 0
    trim_meanqual = 7
    trim_mingc = 0
    trim_maxgc = 0
    trim_tailcrop = 0

    // Variant calling options
    variant_quality = 12
    variant_depth = 10
    variant_position = 0.1
    variant_frequency = 0.05
    variant_significance = 1e-3

    // Haplotyping options
    haplotype_significance = 0.05
    haplotype_depth = 10
    haplotype_frequency = 0.05
    haplotype_method = 'ml-template'
    haplotype_overlap_min = 0
    haplotype_overlap_max = 100
    haplotype_iterations = 1000
    cliquesnv_method = 'accurate'

    // Phylogenetics options
    mafft_method = '--auto'
    phylogenetic_bootstraps = 1000
    phylogenetic_bootstrap_cutoff = 0.03
    phylogenetic_model = 'GTR+G'

    // Step-skipping options
    skip_trimming = false
    skip_qc = false
    skip_filtering = false
    skip_haplotype = false
    skip_phylogenetics = false

    // Remote resource options
    freezetable_js = 'https://cdn.jsdelivr.net/npm/jquery-freeze-table@1.3.0/dist/js/freeze-table.min.js'
    igv_js = 'https://cdn.jsdelivr.net/npm/igv@2.11.0/dist/igv.js'
    phylotree_css = 'https://cdn.jsdelivr.net/npm/phylotree@1.0.13/dist/phylotree.css'
    d3_js = 'https://cdn.jsdelivr.net/npm/d3@5.16.0/dist/d3.min.js'
    underscore_js = 'https://cdn.jsdelivr.net/npm/underscore@1.13.2/underscore-umd.min.js'
    phylotree_js = 'https://cdn.jsdelivr.net/npm/phylotree@1.0.13/dist/phylotree.min.js'

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

    // Boilerplate options
    outdir = null
    tracedir = "${params.outdir}/pipeline_info"
    publish_dir_mode = 'copy'
    email = null
    email_on_fail = null
    plaintext_email = false
    monochrome_logs = false
    breed = 'plain'
    help = false
    validate_params = true
    show_hidden_params = false
    schema_ignore_params = 'genomes'
    enable_conda = false

    // Config options
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact = null
    config_profile_url = null
    config_profile_name = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory = '128.GB'
    max_cpus = 16
    max_time = '240.h'

}

// Load base.config by default for all pipelines
includeConfig 'conf/base.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 nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load nf-core/yavsap custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
//   includeConfig "${params.custom_config_base}/pipeline/yavsap.config"
// } catch (Exception e) {
//   System.err.println("WARNING: Could not load nf-core/config/yavsap profiles: ${params.custom_config_base}/pipeline/yavsap.config")
// }


profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        params.enable_conda    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    gh {
        params {
            max_cpus = 2
            max_memory = '6.GB'
            max_time = '6.h'
        }
    }
    test { includeConfig 'conf/test.config' }
    test_full { includeConfig 'conf/test_full.config' }
    test_interleaved { includeConfig 'conf/test_interleaved.config' } // Illumina PE Interleaved
    test_se { includeConfig 'conf/test_se.config' } // Illumina SE
    test_nanopore { includeConfig 'conf/test_nanopore.config' } // Nanopore
}

// 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 = "\$PWD:/usr/local/share/julia"
}

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

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name = 'yavsap'
    author = 'Thomas A. Christensen II'
    homePage = 'https://ksumngs.github.io/yavsap'
    description = 'Identification and analysis of viral haplotypes in metagenomic NGS reads'
    mainScript = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version = '0.9.1'
    recurseSubmodules = true
}

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

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}