nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                      = null

    // Reference
    reference                  = null

    // ******************* OPTIONAL PROCESSES ******************* //
    // Trimming
    trim                       = true
    save_trimmed_fail          = false
    adapter_file               = "${baseDir}/assets/adapters.fas"

    //When downsampling specifiy the maximum coverage depth
    subsampling_off            = false
    subsampling_depth_cutoff   = 100

    // When downsampling and all samples have the same expected genome size specify as e.g 210820b or 2.1mb
    genome_size                = false

    // Remove recombination using gubbins prior to building tree
    remove_recombination       = false

    //Maximum non GATC bases (i.e - and N) to allow in pseudogenome sequences
    non_GATC_threshold         = 0.5

    // Which tree building alogorithms to use
    rapidnj                    = false
    fasttree                   = false
    iqtree                     = false
    raxmlng                    = false

    // MultiQC
    multiqc_config             = null
    multiqc_title              = null

    // Boilerplate options
    outdir                            = './results'
    tracedir                          = "${params.outdir}/pipeline_info"
    publish_dir_mode                  = 'copy'
    email                             = null
    email_on_fail                     = null
    plaintext_email                   = false
    max_multiqc_email_size            = '25.MB'
    skip_multiqc                      = false
    enable_conda                      = false
    validate_params                   = true
    show_hidden_params                = false
    schema_ignore_params              = 'modules'
    monochrome_logs                   = false
    help                              = false
    singularity_pull_docker_container = false

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

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '16.GB'
    max_cpus                   = 4
    max_time                   = '168.h'

}

// 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")
}

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        conda.enabled          = true
	params.enable_conda    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
	process {
         withName: 'BWA_INDEX|FASTP|SUB_SAMPLING|BAM_SORT_SAMTOOLS|VARIANTS_BCFTOOLS|VCF2PSEUDOGENOME|ALIGNPSEUDOGENOMES|SNPSITES|GUBBINS|CREATE_PHYLOGENY|MULTIQC'{
               conda = "${baseDir}/conda_environments/environment.yml"
         }
         
   }
    }
    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
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.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']

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            = 'nf-core/bactmap'
    author          = 'Anthony Underwood'
    homePage        = 'https://github.com/nf-core/bactmap'
    description     = 'A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version = '1.0.0'
}

// 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
        }
    }
}