nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/seqsubmit Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {

    // Input options
    input                         = null
    mode                          = null  // {mags, bins, metagenomic_assemblies, reads}

    study_metadata                = null
    submission_study              = null
    is_private                    = false
    release_date                  = null
    centre_name                   = null
    upload_tpa                    = false
    test_upload                   = true
    webincli_mode                 = "submit"

    // rna detection
    rrna_limit                    = 80
    trna_limit                    = 18

    // checkm2: completeness and contamination
    checkm2_db                    = null
    checkm2_db_download_id        = 14897628

    // NCBI taxonomy
    cat_db                        = 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
    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
}

// Backwards compatibility for publishDir syntax
outputDir = params.outdir
workflow.output.mode = params.publish_dir_mode

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

// Set container for docker amd64 by default
includeConfig 'conf/containers_docker_amd64.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
    }
    mamba_arm {
        conda.enabled           = true
    }
    mamba_env {
        conda.enabled           = true // Use the environment.yml file in the module main.nf
        conda.useMamba          = true
    }
    docker {
        includeConfig           'conf/containers_docker_amd64.config'
        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)'
    }
    docker_arm {
        includeConfig           'conf/containers_docker_arm64.config'
        docker.enabled          = true
    }
    arm64 {
        process.arch            = 'arm64'
        // Related Issue https://github.com/nf-core/modules/issues/6694
        // For now if you're using arm64 you have to use wave for the sake of the maintainers
        // wave profile
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    emulate_amd64 {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        includeConfig           'conf/containers_singularity_https_amd64.config'
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    singularity_arm {
        includeConfig           'conf/containers_singularity_https_arm64.config'
        singularity.enabled     = true
    }
    singularity_oras {
        includeConfig           'conf/containers_singularity_oras_amd64.config'
        singularity.enabled     = true
    }
    singularity_oras_arm {
        includeConfig           'conf/containers_singularity_oras_arm64.config'
        singularity.enabled     = true
    }
    podman {
        includeConfig           'conf/containers_docker_amd64.config'
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    podman_arm {
        includeConfig           'conf/containers_docker_arm64.config'
        podman.enabled          = true
    }
    shifter {
        includeConfig          'conf/containers_docker_amd64.config'
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter_arm {
        includeConfig           'conf/containers_docker_arm64.config'
        shifter.enabled         = true
    }
    charliecloud {
        includeConfig           'conf/containers_docker_amd64.config'
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    charliecloud_arm {
        includeConfig           'conf/containers_docker_arm64.config'
        charliecloud.enabled    = true
    }
    apptainer {
        includeConfig           'conf/containers_singularity_https_amd64.config'
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    apptainer_arm {
        includeConfig           'conf/containers_singularity_oras_arm64.config'
        singularity.enabled     = true
    }
    apptainer_oras {
        includeConfig           'conf/containers_singularity_oras_amd64.config'
        apptainer.enabled       = true
    }
    apptainer_oras_arm {
        includeConfig           'conf/containers_singularity_oras_arm64.config'
        singularity.enabled     = true
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
    test                                     { includeConfig 'conf/test.config' }
    test_full                                { includeConfig 'conf/test_full.config' }
    test_mag_complete_metadata               { includeConfig 'conf/test_mag_complete_metadata.conf' }
    test_mag_no_study_complete_metadata      { includeConfig 'conf/test_mag_no_study_complete_metadata.config' }
    test_mag_no_coverage_single_reads        { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' }
    test_mag_no_coverage_paired_reads        { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' }
    test_mag_no_quality                      { includeConfig 'conf/test_mag_no_quality.conf' }
    test_mag_one_contig                      { includeConfig 'conf/test_mag_one_contig.conf' }
    test_mag_no_rna_presence                 { includeConfig 'conf/test_mag_no_rna_presence.conf' }
    test_mag_no_taxonomy                     { includeConfig 'conf/test_mag_no_taxonomy.conf' }
    test_assembly_complete_metadata          { includeConfig 'conf/test_assembly_complete_metadata.config' }
    test_assembly_no_study_complete_metadata { includeConfig 'conf/test_assembly_no_study_complete_metadata.config' }
    test_assembly_no_coverage_single_reads   { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' }
    test_assembly_no_coverage_paired_reads   { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' }
    test_assembly_one_contig                 { includeConfig 'conf/test_assembly_one_contig.config' }
    test_reads_paired                        { includeConfig 'conf/test_reads_paired.config' }
}

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/seqsubmit custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"


// Load nf-core/seqsubmit custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/seqsubmit.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"
    ENA_WEBIN          = secrets.ENA_WEBIN
    ENA_WEBIN_PASSWORD = secrets.ENA_WEBIN_PASSWORD
}

// 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/seqsubmit'
    contributors    = [
        [
            name: 'Martin Beracochea',
            affiliation: 'EMBL-EBI',
            email: 'mbc@ebi.ac.uk',
            github: 'https://github.com/mberacochea',
            contribution: ['author', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0003-3472-3736'
        ],
        [
            name: 'Ekaterina Sakharova',
            affiliation: 'EMBL-EBI',
            email: 'kates@ebi.ac.uk',
            github: 'https://github.com/KateSakharova',
            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-6867-2039'
        ],
        [
            name: 'Sofia Ochkalova',
            affiliation: 'EMBL-EBI',
            email: 'sofia@ebi.ac.uk',
            github: 'https://github.com/ochkalova',
            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Timothy Rozday',
            affiliation: 'EMBL-EBI',
            email: 'timrozday@ebi.ac.uk',
            github: 'https://github.com/timrozday-mgnify',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-7016-0665'
        ],
        [
            name: 'Evangelos Karatzas',
            affiliation: 'EMBL-EBI',
            email: 'vangelis@ebi.ac.uk',
            github: 'https://github.com/vagkaratzas',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-9132-8981'
        ]
    ]
    homePage        = 'https://github.com/nf-core/seqsubmit'
    description     = """Submit sequences, assemblies, MAGs, etc., to public archives"""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=25.10.4'
    version         = '1.0.0'
    doi             = ''
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'