nextflow.config

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

// Global default params, used in configs
params {
    // Specify which workflow to run. Options are 'PRE_MYCOSNP' or 'NFCORE_MYCOSNP'
    workflow = 'NFCORE_MYCOSNP'

    // Input options
    input                      = null
    add_sra_file               = null
    add_vcf_file               = null

    // Pre-Mycosnp
    assembler                  = "skesa"
    shovill_depth              = 70
    genome_size                = ''
    min_contig_cov             = 10
    min_contig_len             = 300
    gambit_db                  = "$projectDir/assets/gambit_db/gambit-fungal-metadata-1.0.0-20241213.gdb"
    gambit_h5_dir              = "$projectDir/assets/gambit_db/signatures/"
    subtype_db                 = "$projectDir/assets/sourmash_db/"

    // References
    genome                     = null
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    igenomes_ignore            = false
    snpeffconfig               = "$projectDir/assets/snpeffdb/"
    species                    = 'candida_auris_gca_016772135.1'
    genes                      = 'CAB11_002014'
    positions                  = 'fks1_hs1=221637:221663,fks1_hs2=223782:223805,fks1_hs3=221805:221807'
    exclude                    = 'synonymous_variant'

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

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    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

    // 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                 = '24.GB'
    max_cpus                   = 4
    max_time                   = '240.h'

    // Mycosnp options
    save_reference             = true
    save_alignment             = true
    sample_ploidy              = 1
    coverage                   = 0 // Desired sample coverage used in seqtk_sample, if 0 seqtk_sample will not be preformed.
    // rate                       = 1
    gvcfs_filter               = 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || DP < 10'
    gatkgenotypes_filter        = '--min_GQ "50" --keep_GQ_0_refs --min_percent_alt_in_AD "0.8" --min_total_DP "10" --keep_all_ref'
    max_amb_samples            = 10000000
    max_perc_amb_samples       = 10
    min_depth                  = 10
    publish_dir_mode           = 'copy'
    rapidnj                    = true
    fasttree                   = true
    //snpeff_build               = false
    snpeff                     = false
    iqtree                     = false
    raxmlng                    = false
    save_debug                 = false
    mask                       = true
    skip_samples               = ""
    skip_samples_file          = null
    skip_combined_analysis     = false
    skip_phylogeny             = false

    // Reference files Directory (invalidates specific declarations)
    ref_dir                     = null

    // Reference files and indices - all must be provided if one is provided else run will fail.
    // Will be ignored if using --ref_dir
    ref_masked_fasta            = null
    ref_fai                     = null
    ref_bwa                     = null
    ref_dict                    = null
}

process {
    // MultiQC: set publishDir based on params.workflow
    withName: 'MULTIQC' {
        if (params.workflow == 'PRE_MYCOSNP') {
            publishDir = [
                path: { "${params.outdir}/multiqc/pre-mycosnp" },
                mode: params.publish_dir_mode
            ]
        } else if (params.workflow == 'NFCORE_MYCOSNP') {
            publishDir = [
                path: { "${params.outdir}/multiqc/mycosnp" },
                mode: params.publish_dir_mode
            ]
        }
    }
}

// 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")
}

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
        process.containerOptions = '-u $(id -u):$(id -g)'
    }
    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
    }
    test      	{ includeConfig 'conf/test.config'      }
    test_full 	{ includeConfig 'conf/test_full.config' }
    sge		{ includeConfig 'conf/custom.config'  }
}

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

// 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']

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}.svg"
}

manifest {
    name            = 'CDCgov/mycosnp-nf'
    author          = 'CDC'
    homePage        = 'https://github.com/CDCgov/mycosnp-nf'
    description     = 'MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris. This method prepares the reference, performs quality control, and calls variants using a reference. MycoSNP generates several output files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building and gene variant annotations.'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version = '1.6.3'
}

// 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
        }
    }
}