nextflow.config

/*
========================================================================================
    nf-core/aquascope Nextflow config file
========================================================================================
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {
    // Input options
    input                      = null

    // References
    fasta                      = "${projectDir}/assets/references/SARS-CoV-2.reference.fasta"
    gff			               = "${projectDir}/assets/references/SARS-CoV-2.reference.gff"
    gff3                       = "${projectDir}/assets/references/SARS-CoV-2.reference.gff3"
    bed                        = ""

    // Freyja barcodes and metadata
    //freyja_repeats             = 1000 //default, change it to at minimum 250 to run it faster
    freyja_db_name             = 'freyja_db'
    freyja_barcodes            = null
    freyja_lineages_meta       = null
    varthresh                  = 0.01

    // Samtools Ampliconclip parameters
    save_cliprejects           = false
    save_clipstats             = false

    // Ivar variant calling options
    save_mpileup               = true

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = 'AquaScope-SARS-CoV-2 Quality Report'
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                     = './results'
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    hook_url                   = null
    help                       = false
    version                    = null

    // Schema validation default options
    validationFailUnrecognisedParams = false
    validationLenientMode            = true
    validationSchemaIgnoreParams     = 'genomes,igenomes_base,monochromeLogs'
    validationShowHiddenParams       = false
    validate_params                  = false
    enable_conda                     = false
    singularity_pull_docker_container= false

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

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

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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")
}
singularity.registry  = 'quay.io'

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
        docker.registry        = 'quay.io'
    }
    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
    }
    scicomp_rosalind        { includeConfig   'conf/scicomp.config'}
    test_illumina   { includeConfig   'conf/test_illumina.config' }
    test_ont        { includeConfig   'conf/test_ont.config'}
    test_bam        { includeConfig   'conf/test_bam.config'}
    test_iontorrent { includeConfig   'conf/test_iontorrent.config' }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

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

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

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 {
    name            = 'CDCGov-Aquascope'
    author          = 'Arun Boddapati, Hunter Seabolt, CDC SciComp'
    homePage        = 'https://github.com/CDCgov/aquascope'
    description     = 'Pipeline is for early detection of SC2 variants of concern via shotgun metagenomic sequencing of wastewater'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.02'
    version         = '3.0'
    doi             = ' '
}

// setting plugins 
plugins {
    id 'nf-schema@2.3.0'
}