nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/pathogensurveillance Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/


// Global default params, used in configs
params {

    // Input options
    input                        = null
    reference_data               = null
    bakta_db                     = null
    temp_dir                     = null
    data_dir                     = 'path_surveil_data'
    download_bakta_db            = true
    max_depth                    = 100
    only_latin_binomial_refs     = false
    allow_non_refseq             = false
    allow_atypical_refs          = false
    allow_unannotated            = false
    n_ref_strains                = 5
    n_ref_species                = 20
    n_ref_genera                 = 10
    n_ref_closest                = 2
    n_ref_closest_named          = 1
    n_ref_context                = 5
    ref_min_ani                  = 0.95
    phylo_min_genes              = 30
    phylo_max_genes              = 300
    bakta_db_type                = 'light'
    min_bases_to_assemble        = 100000
    max_variants                 = 100000

    // 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'
    copymode                     = 'medium'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    hook_url                     = null
    help                         = false
    help_full                    = false
    validate_params              = true
    show_hidden_params           = false
    hpc_queue                    = null
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
    config_profile_name          = null
    config_profile_description   = null

    custom_config_version        = 'master'
    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact       = null
    config_profile_url           = null
    config_profile_name          = null

    // Max total options for all jobs combined
    max_total_memory             = null
    max_total_cpus               = null
    max_total_jobs               = null

    // Schema validation default options
    validate_params              = true
}

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

executor.cpus = params.max_total_cpus
executor.memory = params.max_total_memory
executor.queueSize = params.max_total_jobs

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        conda.channels          = ['conda-forge', 'bioconda']
        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
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    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
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                memory: 8.GB,
                cpus  : 4,
                time  : 1.h
            ]
        }
    }
    slurm {
        executor.name = 'slurm' // Use SLURM for job scheduling
        executor.memory = 200.GB
        process.queue = params.hpc_queue // SLURM partition
        executor.clusterOptions = '--qos=normal' // Additional SLURM options
        executor.perCpuMemAllocation = false // Enable per-CPU memory allocation if required by the cluster
    }
    xanthomonas                 { includeConfig 'conf/xanthomonas.config' }
    xanthomonas_small           { includeConfig 'conf/xanthomonas_small.config' }
    ramorum_small               { includeConfig 'conf/ramorum_small.config' }
    mixed                       { includeConfig 'conf/mixed.config' }
    mixed_bacteria              { includeConfig 'conf/mixed_bacteria.config' }
    mycobacteroides             { includeConfig 'conf/mycobacteroides.config' }
    mycobacteroides_small       { includeConfig 'conf/mycobacteroides_small.config' }
    high_complexity_kpneumoniae { includeConfig 'conf/high_complexity_kpneumoniae.config' }
    wagner_2023                 { includeConfig 'conf/wagner_2023.config' }
    wagner_2023_small           { includeConfig 'conf/wagner_2023_small.config' }
    chaos                       { includeConfig 'conf/chaos.config' }
    aps_workshop                { includeConfig 'conf/aps_workshop.config' }
    test                        { includeConfig 'conf/test.config' }
    test_full                   { includeConfig 'conf/test_full.config' }
    ppluvialis                  { includeConfig 'conf/ppluvialis.config' }
    complex_small               { includeConfig 'conf/complex_small.config' }
    complex_minimal             { includeConfig 'conf/complex_minimal.config' }
    complex                     { includeConfig 'conf/complex.config' }
    cqls                        { includeConfig 'conf/cqls.config' }
    testserratia_38             { includeConfig 'conf/testserratia_38.config' }
    serratia_N664               { includeConfig 'conf/serratia_N664.config'}
    serratia_small              { includeConfig 'conf/serratia_small.config'}
    small_genome                { includeConfig 'conf/small_genome.config' }
    salmonella                  { includeConfig 'conf/salmonella.config' }
}

// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load nf-core/pathogensurveillance custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pathogensurveillance.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / 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'
charliecloud.registry = 'quay.io'

// 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"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'nf-core/pathogensurveillance'
    author          = """Zachary S.L. Foster, Camilo Parada-Rojas, Logan Blair, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Ricardo Alcalá-Briseño, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald"""
    contributors    = [
        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
        [
            name: 'Zachary S.L. Foster',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Martha Sudermann',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Nicholas C. Cauldron',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Fernanda I. Bocardo',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Hung Phan',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Jeff H. Chang',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Niklaus J. Grünwald',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
    ]
    homePage        = 'https://github.com/nf-core/pathogensurveillance'
    description     = """Surveillance of pathogens using high-throughput sequencing"""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=24.04.2'
    version         = '1.0.0'
    doi             = ''
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
    help {
        enabled = true
        command = "nextflow run nf-core/pathogensurveillance -profile <docker/singularity/.../institute> --input samplesheet.tsv --outdir <OUTDIR>"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
        beforeText = """
-\033[2m----------------------------------------------------\033[0m-
                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                        \033[0;32m`._,._,\'\033[0m
\033[0;35m  nf-core/pathogensurveillance ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/pathogensurveillance/blob/main/CITATIONS.md
"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText = validation.help.afterText
    }
}

def check_prio(copymode_level, copy_priority) {
    if (copymode_level == 'high') {
        return 'copy'
    } else if (copymode_level == 'medium' && copy_priority != 'low') {
        return 'copy'
    } else {
        return 'symlink'
    }
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'