nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    ebi-metagenomics/mettannotator Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    input                      = null
    // Fast mode //
    fast                       = false

    // Reference databases //

    // Folder for the auto db download step
    dbs                            = null

    interproscan_db                = null
    interproscan_db_version        = "5.62-94.0"

    interpro_entry_list            = null
    interpro_entry_list_version    = "94"

    eggnog_db                      = null
    eggnog_db_version              = "5.0.2"

    amrfinder_plus_db              = null
    amrfinder_plus_db_version      = "2024-01-31.1"

    defense_finder_db              = null
    defense_finder_db_version      = "1.2.3"

    antismash_db                   = null
    antismash_db_version           = "7.1.0"

    dbcan_db                       = null
    dbcan_db_version               = "4.1.3_V12"

    rfam_ncrna_models              = null
    rfam_ncrna_models_rfam_version = "14.9"

    bakta_db                       = null
    bakta_db_version               = "2024-01-19"

    pseudofinder_db                = null
    pseudofinder_db_version        = "2024_06"

   // Tool options
    bakta                          = false

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

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

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

    // Each profile is responsible for using this setting
    singularity_cachedir       = ''

    // Schema validation default options
    validationFailUnrecognisedParams = false
    validationLenientMode            = false
    validationSchemaIgnoreParams     = ''
    validationShowHiddenParams       = false
    validate_params                  = true

}

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

profiles {
    debug {
        dumpHashes             = true
        process.beforeScript   = 'echo $HOSTNAME'
        cleanup                = false
    }
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    mamba {
        conda.enabled          = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    arm {
        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    podman {
        podman.enabled         = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    shifter {
        shifter.enabled        = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    charliecloud {
        charliecloud.enabled   = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        apptainer.enabled      = false
    }
    apptainer {
        apptainer.enabled      = true
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    gitpod {
        executor.name          = 'local'
        executor.cpus          = 16
        executor.memory        = 60.GB
    }
    test { includeConfig 'conf/test.config' }

    local {
        params {
            // Any modern laptop / desktop should have at least...
            max_memory = "12GB"
            max_cpus   = 8
        }
    }

    ebi {
        params.workdir = "/hps/nobackup/rdf/metagenomics/service-team/nextflow-workdir/mett-pipeline"
        params.singularity_cachedir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"

        workDir = params.workdir

        includeConfig 'conf/ebi_codon.config'

        singularity {
            enabled = true
            autoMounts = true
            cacheDir = params.singularity_cachedir
        }

        process {
            cache = "lenient"
            errorStrategy = {
                task.exitStatus in ((130..145) + 104 + 247 + 250) && task.attempt <= 2 ? 'retry' : 'finish'
            }
        }
    }

    ebi_lsf {
        executor {
            name = "lsf"
            queueSize = 200
            submitRateLimit = "10 sec"
            pollInterval = "10 sec"
        }
        process {
            queue = {
                task.memory >= 200.GB ? 'bigmem' : 'production'
            }
        }
    }

    ebi_slurm {
        executor {
            name = "slurm"
            queueSize = 200
            queueGlobalStatus = true
            submitRateLimit = "10 sec"
            pollInterval = "10 sec"
        }
    }

    // EMBL Heidelberg
    embl_hd {
        includeConfig 'conf/embl_hd.config'
    }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry   = 'quay.io'
docker.registry      = 'quay.io'
podman.registry      = 'quay.io'
singularity.registry = 'quay.io'

// Nextflow plugins
plugins {
    id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a assemblies sheet
}

// 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    = "${params.outdir}/pipeline_info/execution_timeline_${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            = 'ebi-metagenomics/mettannotator'
    author          = """@mberacochea,@tgurbich"""
    homePage        = 'https://github.com/ebi-metagenomics/mettannotator'
    description     = """ME TT assembly annotation pipeline"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '1.4.0'
    doi             = 'https://doi.org/10.1101/2024.07.11.603040'
}

// 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
        }
    }
}