nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    phac-nml/viralassembly Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {
    // Pick a variant caller from [medaka, clair3, nanopolish]
    variant_caller = ''

    // Required input file/directory (one or the other)
    input = ''
    fastq_pass = ''

    // Optional Inputs (fast5_pass and sequencing_summary needed for nanopolish)
    metadata = ''
    fast5_pass = ''
    sequencing_summary = ''

    // Medaka if using
    medaka_model = 'r941_min_hac_g507'

    // Clair3 if using
    clair3_model = 'r941_prom_sup_g5014'
    clair3_user_variant_model = ''
    clair3_no_pool_split = false

    // Read filtering options
    min_reads = 20
    min_length = 200
    max_length = 3000

    // Scheme options
    reference = '' // Turns off scheme when passed
    scheme = ''
    scheme_version = ''
    scheme_repo = 'https://github.com/artic-network/primer-schemes.git'
    local_scheme = ''

    // Artic Minion options
    normalise = 1000
    no_frameshift = false
    use_bwa = false
    skip_longshot = false

    // Use the python-based artic pipeline over nextflow one
    use_artic_tool = false

    // SnpEFF
    //  Must match reference id to generate annotations
    //  Will attempt to automatically do so
    skip_snpeff = false
    gff = ''

    // Sample QC and Checks
    skip_qc = false
    pcr_primer_bed = ''
    neg_control_threshold = 0.10
    neg_ctrl_substrings = 'neg,ntc,blank' // Substring of values separated by a , to seach for in sample names

    // MultiQC or Custom Report (which has no singularity env at the moment)
    custom_report = false
    multiqc_config_overall = "$projectDir/assets/multiqc_config_overall.yaml"
    multiqc_config_sample = "$projectDir/assets/multiqc_config_sample.yaml"

    // Other options
    outdir = 'results'
    cache = ''
    help = false
    version = false
    show_hidden_params = false
    monochrome_logs = false

    // Max resource options
    max_memory = '256.GB'
    max_cpus = 16
    max_time = '120.h'

}

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

profiles {
    debug {
        dumpHashes             = true
        process.beforeScript   = 'echo $HOSTNAME'
        cleanup                = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        channels               = ['conda-forge', 'bioconda', 'defaults']
        apptainer.enabled      = false
        // Use cache if arg given
        if ( params.cache ) {
            conda.cacheDir = params.cache
        }
    }
    mamba {
        conda.enabled          = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        // Use cache if arg given
        if ( params.cache ) {
            conda.cacheDir = params.cache
        }
    }
    docker {
        docker.enabled         = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        docker.runOptions      = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        // Use cache if arg given
        if ( params.cache ) {
            singularity.cacheDir = params.cache
        }
    }
    podman {
        podman.enabled         = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    shifter {
        shifter.enabled        = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    charliecloud {
        charliecloud.enabled   = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        apptainer.enabled      = false
    }
    apptainer {
        apptainer.enabled      = true
        apptainer.autoMounts   = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    gitpod {
        executor.name          = 'local'
        executor.cpus          = 4
        executor.memory        = 8.GB
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
    nml { includeConfig 'conf/nml.config'             }
}

// 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'

// Nextflow plugins - When I have a chance to adjust inputs
plugins {
    id 'nf-schema@2.0.0'
}

// 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"
}

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

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

// Manifest information
manifest {
    name            = 'phac-nml/viralassembly'
    author          = """Darian Hole"""
    homePage        = 'https://github.com/phac-nml/viralassembly'
    description     = """Assemble and QC viral reads"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '1.1.0'
    doi             = ''
    defaultBranch   = 'main'
}

// Load modules.config for DSL2 module specific options
//  ToDo - Probably have to convert more args to the modules config
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
        }
    }
}