nextflow.config

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

// Global default params, used in configs
params {
    // Input/output options
    input                         = null
    save_intermediates            = false

    // Unify options
    unify_gene_symbols            = false
    duplicate_var_resolution      = 'sum'
    force_obs_cols                = ''
    aggregate_isoforms            = false

    // Quality control options
    species                       = 'human'
    cell_cycle_scoring            = true
    s_genes                       = null
    g2m_genes                     = null
    mito_genes                    = null
    ambient_correction            = 'soupx'
    use_ambient_corrected_counts  = false
    doublet_detection             = 'scdblfinder'
    doublet_detection_threshold   = 1
    doublet_removal               = false
    empty_droplet_removal         = 'cellbender'
    emptydrops_lower              = 100
    emptydrops_fdr                = 0.01
    cellbender_epochs             = 150

    // Sampling options
    sample_n                      = null
    sample_fraction               = null

    // Integration options
    feature_selection             = 'deviance'
    normalization_method          = 'scran'
    integration_methods           = 'scvi'
    integration_n_features        = 0
    integration_excluded_genes    = null
    scvi_model                    = null
    scanvi_model                  = null
    scimilarity_model             = 'https://zenodo.org/records/10685499/files/model_v1.1.tar.gz'
    symphony_reference            = null
    expimap_gmt                   = null

    // Extension options
    base_adata                    = null
    base_embeddings               = null
    base_label_col                = 'label'
    base_condition_col            = 'condition'
    base_donor_col                = 'donor'
    integrate_per_label           = false
    integrate_per_label_whitelist = null

    // Clustering options
    clustering_resolutions        = '0.25,0.5,1.0'
    neighbors_n_pcs               = null
    tsne                          = false
    cluster_per_label             = false
    cluster_global                = true
    analysis_plan                 = null

    // Pipeline options
    qc_only                       = false
    skip_liana                    = false
    liana_n_perms                 = 1000
    liana_max_cells               = null
    liana_subsample_strategy      = 'stratified_obs'
    liana_subsample_seed          = 42
    cell2cell                     = false
    cell2cell_rank                = null
    cell2cell_seed                = 42
    skip_qc_report                = false
    scib                          = false
    scib_max_cells                = null
    scib_subsample_strategy       = 'stratified_label_batch'
    scib_subsample_seed           = 42
    scib_metric_profile           = 'fast'
    de_methods                    = 'wilcoxon'
    interesting_genes             = null
    pseudobulk                    = false
    prep_cellxgene                = false
    tords                         = false

    // scVI options
    scvi_n_latent                 = 30
    scvi_n_hidden                 = 128
    scvi_n_layers                 = 2
    scvi_dispersion               = 'gene'
    scvi_gene_likelihood          = 'zinb'
    scvi_max_epochs               = null
    scvi_categorical_covariates   = ''
    scvi_continuous_covariates    = ''
    scvi_use_observed_lib_size    = true

    // Pseudobulking options
    pseudobulk_min_num_cells      = 10
    pseudobulk_min_total_counts   = 1000
    reference_condition           = ''

    // Pathway analysis options
    decoupler                     = false
    decoupler_resources           = 'progeny,collectri'
    decoupler_network             = null
    decoupler_method              = 'ulm'
    decoupler_min_targets         = 5

    // Resource options
    memory_scale                  = 1

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

    // Celltype assignment options
    celltypist_model              = null
    azimuth                       = false
    celldex_reference             = null
    cytetype_study_context        = 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/4d8b9974c14cf11280d29bfe16f94e284793e499/'
    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'

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'
    }
    python_only {
        includeConfig 'conf/python_only.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/scdownstream 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"

// 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"
    // anndataR cannot read nullable-string-array encodings yet, so all writers use the legacy format
    ANNDATA_ALLOW_WRITE_NULLABLE_STRINGS = 0
    // Intel OpenMP CPU topology detection fails on macOS
    KMP_AFFINITY                         = "disabled"
    // Container home directories are read-only, so caches must live in the task directory
    NUMBA_CACHE_DIR                      = "./tmp/numba"
    MPLCONFIGDIR                         = "./tmp/matplotlib"
}

// Set bash options
process.shell = [
    "bash",
    "-C",
    "-e",
    "-u",
    "-o",
    "pipefail",
]

// 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/scdownstream'
    contributors    = [
        [
            name: 'Nico Trummer',
            affiliation: 'Technical University of Munich',
            email: 'nico.trummer@tum.de',
            github: '@nictru',
            contribution: ['author', 'maintainer'],
            orcid: '0000-0002-4639-0935',
        ],
        [
            name: 'Leon Hafner',
            affiliation: 'Technical University of Munich',
            email: '',
            github: '@LeonHafner',
            contribution: ['contributor'],
            orcid: '0000-0002-2705-1727',
        ],
        [
            name: 'Erik Fasterius',
            affiliation: 'National Bioinformatics Infrastructure Sweden',
            email: '',
            github: '@fasterius',
            contribution: ['contributor'],
            orcid: '0000-0003-0492-9960',
        ],
    ]
    homePage        = 'https://github.com/nf-core/scdownstream'
    description     = """A single cell transcriptomics pipeline for QC, integration and making the results presentable"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=26.04.6'
    version         = '0.0.1dev'
    doi             = ''
    diagram         = 'docs/images/metromap.svg'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1'
    id 'nf-anndata@0.5.2'
}

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