nextflow.config

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

// Global default params, used in configs
params {

    // Global parameters
    input                      = null
    outdir                     = null
    project_title              = ''
    genome                     = null
    ncbi_fasta                 = null
    ncbi_fai                   = null
    ncbi_dict                  = null
    ucsc_fasta                 = null
    ucsc_fai                   = null
    ucsc_dict                  = null
    gene_annotation            = null
    hpo_file                   = null
    random_seed                = false

    // Export counts
    ec_gene_annotations        = null
    ec_exclude_groups          = null

    // Aberrant expression
    ae_skip                    = false
    ae_groups                  = ""
    ae_min_ids                 = 1
    ae_fpkm_cutoff             = 1
    ae_implementation          = "autoencoder"
    ae_z_score_cutoff          = 0
    ae_padj_cutoff             = 0.05
    ae_max_tested_dimension_proportion = 3
    ae_yield_size              = 2000000
    ae_genes_to_test           = null
    ae_use_grid_search_to_obtain_q = false

    // Aberrant splicing
    as_skip                    = false
    as_groups                  = ""
    as_min_ids                 = 1
    as_recount                 = false
    as_long_read               = false
    as_keep_non_standard_chrs  = false
    as_skip_filter             = false
    as_min_expression_in_one_sample = 20
    as_quantile_min_expression = 10
    as_quantile_for_filtering  = 0.75
    as_min_delta_psi           = 0.05
    as_implementation          = "PCA"
    as_fraser_version          = "FRASER2"
    as_delta_psi_cutoff        = 0.3
    as_padj_cutoff             = 0.1
    as_max_tested_dimension_proportion = 6
    as_genes_to_test           = null
    as_use_grid_search_to_obtain_q = false

    // Mono-allelic expression
    mae_skip                   = false
    mae_groups                 = null
    mae_gatk_header_check      = false
    mae_padj_cutoff            = 0.05
    mae_allelic_ratio_cutoff   = 0.8
    mae_add_af                 = false
    mae_max_af                 = 0.001
    mae_max_var_freq_cohort    = 0.05
    mae_qc_vcf                 = null
    mae_qc_vcf_tbi             = null
    mae_qc_groups              = null
    mae_dna_rna_match_cutoff   = 0.05

    // References
    igenomes_base              = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore            = false

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

    // Boilerplate options
    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
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/drop/data/'
    modules_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/'
    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
}

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

profiles {
    debug {
        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
        conda.createTimeout     = '2 h'
    }
    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/drop 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/drop custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/drop.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/drop'
    contributors    = [
        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
        [
            name: 'Michaela Mueller',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Vicente Yepez',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Christian Mertes',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Daniela Andrade',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Cristian Sandu',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Andrew Behrens',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: ' Julien Gagneur',
            affiliation: '',
            email: '',
            github: '',
            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
    ]
    homePage        = 'https://github.com/nf-core/drop'
    description     = """The detection of RNA Outliers Pipeline (DROP) is an integrative workflow to detect aberrant expression, aberrant splicing, and mono-allelic expression from raw sequencing files."""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.0'
    version         = '1.0dev'
    doi             = ''
}

// Nextflow plugins
plugins {
    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'