nextflow.config

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

// Global default params, used in configs
params {
    // Input options
    input                        = null
    sample_size                  = 0
    skip_tools                   = ''

    // References
    genome                       = null
    igenomes_base                = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore              = false
    sort_bam                     = true

    // Fastqscreen options
    fastq_screen_references      = "${projectDir}/assets/example_fastq_screen_references.csv"

    // 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                     = System.getenv('HOOK_URL')
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
    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')

    // picard_collecthsmetrics options
    run_picard_collecthsmetrics  = false
    bait_intervals               = null
    target_intervals             = null

    // 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
}

// 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)'
    }
    arm64 {
        process.arch            = 'arm64'
        // TODO 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 {
        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'
    }
    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'
    }
}

// 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/seqinspector 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/seqinspector 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/seqinspector.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'

// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'

// 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/seqinspector'
    contributors    = [
        [
            name: 'Adrien Coulier',
            affiliation: 'Pixelgen Technologies',
            github: 'Aratz',
            contribution: ['author'],
            orcid: '0000-0003-2702-1103',
        ],
        [
            name: 'Alfred Kedhammar',
            affiliation: 'Clinical Genomics',
            github: 'kedhammar',
            contribution: ['author'],
        ],
        [
            name: 'Agrima Bhatt',
            affiliation: 'National Genomics Infrastructure',
            github: 'agrima2010',
            contribution: ['author'],
            orcid: '0009-0004-5536-7210',
        ],
        [
            name: 'Maxime U Garcia',
            affiliation: 'National Genomics Infrastructure',
            github: 'maxulysse',
            contribution: ['contributor', 'maintainer'],
            orcid: '0000-0003-2827-9261',
        ],
        [
            name: 'Natalia Garcia Garcia',
            github: 'nggvs',
            contribution: ['contributor'],
        ],
        [
            name: 'Franziska Bonath',
            affiliation: 'National Genomics Infrastructure',
            github: 'FranBonath',
            contribution: ['author'],
            orcid: '0000-0002-1270-1504',
        ],
        [
            name: 'Pontus Höjer',
            affiliation: 'National Genomics Infrastructure',
            github: 'pontushojer',
            contribution: ['contributor'],
            orcid: '0000-0001-8010-4755',
        ],
        [
            name: 'Edmund Miller',
            affiliation: 'Seqera',
            github: 'edmundmiller',
            contribution: ['contributor'],
        ],
        [
            name: 'Mahesh Binzer-Panchal',
            affiliation: 'National Bioinformatics Infrastructure Sweden',
            github: 'mahesh-panchal',
            contribution: ['contributor'],
            orcid: '0000-0003-1675-0677',
        ],
        [
            name: 'Ramprasad Neethiraj',
            affiliation: 'Clinical Genomics',
            github: 'ramprasadn',
            contribution: ['author'],
        ],
        [
            name: 'Matilda Åslin',
            affiliation: 'National Genomics Infrastructure',
            github: 'matrulda',
            contribution: ['author'],
        ],
        [
            name: 'Patricie Skaláková',
            affiliation: 'Masaryk University',
            github: 'Patricie34',
            contribution: ['contributor'],
        ],
        [
            name: 'Eliott Bosshard',
            affiliation: 'Clinical Genomics',
            github: 'EliottBo',
            contribution: ['contributor'],
        ],
        [
            name: 'Karthik Nair',
            affiliation: 'National Genomics Infrastructure',
            github: 'KarNair',
            contribution: ['contributor'],
        ],
        [
            name: 'Matthias Zepper',
            affiliation: 'National Genomics Infrastructure',
            github: 'MatthiasZepper',
            contribution: ['author'],
        ],
        [
            name: 'Nelly Nyawira Nkonge',
            affiliation: 'National Genomics Infrastructure',
            github: 'nkongenelly',
            contribution: ['contributor'],
        ],
        [
            name: 'Beatriz Vinhas',
            affiliation: 'Clinical Genomics',
            github: 'beatrizsavinhas',
            contribution: ['contributor'],
        ],
        [
            name: 'Júlia Mir Pedrol',
            affiliation: 'Center For Genomics Regulation',
            github: 'mirpedrol',
            contribution: ['contributor'],
        ],
        [
            name: 'Cristina Tuñí i Domínguez',
            affiliation: 'Flowmics',
            github: 'ctuni',
            contribution: ['contributor'],
        ],
        [
            name: 'Johannes Alneberg',
            affiliation: 'National Genomics Infrastructure',
            github: 'alneberg',
            contribution: ['contributor'],
        ],
        [
            name: 'Annick Renevey',
            affiliation: 'Clinical Genomics',
            github: 'rannick',
            contribution: ['contributor'],
        ],
        [
            name: 'Adam Talbot',
            affiliation: 'Seqera',
            github: 'adamrtalbot',
            contribution: ['contributor'],
        ],
        [
            name: 'Jonas Kjellin',
            affiliation: 'National Genomics Infrastructure',
            github: 'kjellinjonas',
            contribution: ['contributor'],
        ],
        [
            name: 'Tori Griffin',
            affiliation: 'National Genomics Infrastructure',
            github: 'torigiffin',
            contribution: ['contributor'],
        ],
    ]
    homePage        = 'https://github.com/nf-core/seqinspector'
    description     = """Pipeline to QC your sequences"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.2'
    version         = '1.0.0'
    doi             = '10.5281/zenodo.18757486'
}

// Nextflow plugins
plugins {
    id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
    id 'nf-schema@2.6.1'     // 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'