nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Assemblage Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// Global default params, used in configs
params {

	// Input
	input			= null
	
	// QC and trimming options
	phred_score		= "15"
	error_rate		= "0.1"
	minlength		= "20"
	kraken_db		= null
	output_trimmed_reads	= null
	output_kraken_reports   = null

	// Filtering options
	keep_percent		= "90"
	min_read_length		= "1000"

	// Subsampling options
	genome_size		= null
	coverage		= "100"
	output_subsampled_reads = null

	// Assembly options
	unicycler_mode		= "normal"
	min_contig_len		= "500"
	depth_filter		= "0.25"
	unicycler_args		= ""

	// Mapping options
	output_bam		= null
	output_coverage_reports = null

	// Plasmid characterization
	ellipsis		= null
	databases		= null
	species			= null
	mincov			= 0.6
	identity_threshold	= 0.8
	output_mge_reports	= null

	// Pipeline options
	publish_dir_mode	= "copy"
	time_multiplier		= 1
}

// Define profiles
profiles {
    conda {
        params.enable_conda    = true
        apptainer.enabled      = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        apptainer.enabled      = false
	params.enable_conda    = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        apptainer.enabled      = false
	params.enable_conda    = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        apptainer.enabled      = false
	params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        apptainer.enabled      = false
	params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        apptainer.enabled      = false
	params.enable_conda    = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    apptainer {
	apptainer.enabled      = true
        apptainer.autoMounts   = true
        singularity.enabled    = false
        params.enable_conda    = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
}

conda { createTimeout = "120 min" }

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

// Define variables to prevent local R libraries from conflicting with the container
env {
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

// 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
        }
    }
}