nextflow.config

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

// Global default params, used in configs
params {

    // TODO nf-core: Specify your pipeline's command line flags
    // Input options
    input                        = null

    // 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
    help_full                    = false
    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

    // Schema validation default options
    validate_params              = true

    // General parameters
    dbname                       = null
    save_concatenated_fastas     = false

    accession2taxid              = null
    prot2taxid                   = null
    nucl2taxid                   = null
    nodesdmp                     = null
    namesdmp                     = null
    malt_mapdb                   = null

    // tool specific options
    build_bracken                = false
    build_centrifuge             = false
    build_diamond                = false
    build_ganon                  = false
    build_kaiju                  = false
    kaiju_keepintermediate       = false
    build_kraken2                = false
    kraken2_keepintermediate     = false
    build_krakenuniq             = false
    krakenuniq_keepintermediate  = false
    build_malt                   = false

    bracken_build_options         = ''
    centrifuge_build_options      = ''
    diamond_build_options         = ''
    ganon_build_options           = ''
    kaiju_build_options           = ''
    kraken2_build_options         = ''
    krakenuniq_build_options      = ''
    malt_build_options            = "--sequenceType DNA"
}

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

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) --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
        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,
            ]
        }
    }
    test {
        includeConfig 'conf/test.config'
    }
    test_full {
        includeConfig 'conf/test_full.config'
    }
    test_nothing {
        includeConfig 'conf/test_nothing.config'
    }
    test_alternatives {
        includeConfig 'conf/test_alternatives.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/createtaxdb custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/createtaxdb.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/createtaxdb'
    author          = """James A. Fellows Yates and the nf-core community"""
    contributors    = [
        [
            name: 'James A. Fellows Yates',
            affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
            email: 'jfy133@gmail.com',
            github: 'https://github.com/jfy133',
            contribution: ['author', 'maintainer'],
            orcid: 'https://orcid.org/0000-0001-5585-6277',
        ],
        [
            name: 'Alexander Ramos Díaz',
            affiliation: '',
            email: '',
            github: 'https://github.com/alxndrdiaz',
            contribution: ['contributor'],
            orcid: 'https://orcid.org/0000-0001-6410-3349',
        ],
        [
            name: 'Lili Andersson-Li',
            affiliation: 'Karolinska Institutet; Karolinska University Hospital; Clinical Genomics SciLifeLab, Solna',
            email: '',
            github: 'https://github.com/LilyAnderssonLee',
            contribution: ['contributor'],
            orcid: 'https://orcid.org/0000-0002-6059-4192',
        ],
        [
            name: 'Sam Wilkinson',
            affiliation: 'University of Birmingham, Birmingham, United Kingdom',
            email: '',
            github: 'https://github.com/BioWilko',
            contribution: ['contributor'],
            orcid: 'https://orcid.org/0000-0002-6944-5927',
        ],
        [
            name: ' and the nf-core community',
            affiliation: '',
            email: '',
            github: 'https://github.com/nf-core',
            contribution: ['contributor'],
            orcid: '',
        ],
    ]
    homePage        = 'https://github.com/nf-core/createtaxdb'
    description     = """Parallelised and automated creation of metagenomic classifier databases of different tools"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=24.04.2'
    version         = '1.0dev'
    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/createtaxdb -profile <docker/singularity/.../institute> --input samplesheet.csv --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/createtaxdb ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText           = """${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/createtaxdb/blob/master/CITATIONS.md
"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText  = validation.help.afterText
    }
}

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