nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                      = null
    single_end                 = false

    // short read preprocessing options
    save_trimmed_fail          = false
    fastp_qualified_quality    = 15
    fastp_cut_mean_quality     = 15
    keep_phix                  = false
    // phix_reference           = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
    phix_reference             = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
    host_fasta                 = null
    host_genome                = null
    host_removal_verysensitive = false
    host_removal_save_ids      = false

    // binning options
    binning_map_mode           = 'group'
    skip_binning               = false
    min_contig_size            = 1500
    min_length_unbinned_contigs = 1000000
    max_unbinned_contigs       = 100
    skip_prokka                = false

    // assembly options
    coassemble_group           = false
    spades_options             = ''
    megahit_options            = ''
    skip_spades                = false
    skip_spadeshybrid          = false
    skip_megahit               = false
    skip_quast                 = false
    skip_prodigal              = false

    // taxonomy options
    centrifuge_db              = null
    kraken2_db                 = null
    skip_krona                 = false
    cat_db                     = null
    cat_db_generate            = false
    save_cat_db                = false
    gtdb                       = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz"
    gtdbtk_min_completeness    = 50.0
    gtdbtk_max_contamination   = 10.0
    gtdbtk_min_perc_aa         = 10
    gtdbtk_min_af              = 0.65
    gtdbtk_pplacer_cpus        = 1
    gtdbtk_pplacer_scratch     = true

    // long read preprocessing options
    skip_adapter_trimming      = false
    keep_lambda                = false
    longreads_min_length       = 1000
    longreads_keep_percent     = 90
    longreads_length_weight    = 10
    // lambda_reference         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Escherichia_virus_Lambda/all_assembly_versions/GCA_000840245.1_ViralProj14204/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
    lambda_reference           = "${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz"

    // Bin QC
    skip_busco                 = false
    busco_reference            = null
    busco_download_path        = null
    busco_auto_lineage_prok    = false
    save_busco_reference       = false

    // Reproducibility options
    megahit_fix_cpu_1          = false
    spades_fix_cpus            = -1
    spadeshybrid_fix_cpus      = -1
    metabat_rng_seed           = 1

    // References
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    igenomes_ignore            = false

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

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'copy'
    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,modules'
    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

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '128.GB'
    max_cpus                   = 16
    max_time                   = '240.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")
}

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

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
    }
    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_host_rm        { includeConfig 'conf/test_host_rm.config'        }
    test_hybrid         { includeConfig 'conf/test_hybrid.config'         }
    test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
    test_busco_auto     { includeConfig 'conf/test_busco_auto.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/mag'
    author          = 'Hadrien Gourlé, Daniel Straub, Sabrina Krakau'
    homePage        = 'https://github.com/nf-core/mag'
    description     = 'Assembly, binning and annotation of metagenomes'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version         = '2.1.1'
}

// 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
        }
    }
}

// Functions to fix number of cpus to allow reproducibility for MEGAHIT and SPAdes
// if corresponding parameters are specified, number of cpus is not increased with retries
def check_megahit_cpus (x, attempt ) {
    if (params.megahit_fix_cpu_1) return 1
    else return check_max (x * attempt, 'cpus' )
}
def check_spades_cpus (x, attempt ) {
    if (params.spades_fix_cpus != -1) return check_max (params.spades_fix_cpus, 'cpus' )
    else return check_max (x * attempt, 'cpus' )
}
def check_spadeshybrid_cpus (x, attempt ) {
    if (params.spadeshybrid_fix_cpus != -1) return check_max (params.spadeshybrid_fix_cpus, 'cpus' )
    else return check_max (x * attempt, 'cpus' )
}