nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                      = null
    study_name                 = 'study'
    study_type                 = 'rnaseq'
    study_abundance_type       = 'counts'
    contrasts                  = null
    querygse                   = null
    matrix                     = null
    transcript_length_matrix   = null
    control_features           = null
    sizefactors_from_controls  = false

    // Experimental analysis options
    tools   = null
    pathway = null

    // Reporting
    logo_file               = "$projectDir/docs/images/nf-core-differentialabundance_logo_light.png"
    css_file                = "$projectDir/assets/nf-core_style.css"
    citations_file          = "$projectDir/CITATIONS.md"
    report_file             = "$projectDir/assets/differentialabundance_report.Rmd"
    report_title            = null
    report_author           = null
    report_contributors     = null
    report_description      = null
    report_scree            = true
    report_round_digits     = 4

    // Sample sheet options
    observations_type          = 'sample'
    observations_id_col        = 'sample'
    observations_name_col      = null

    // Feature options
    features                    = null
    features_type               = 'gene'
    features_id_col             = 'gene_id'
    features_name_col           = 'gene_name'
    features_metadata_cols      = 'gene_id,gene_name,gene_biotype'

    // GTF parsing options
    features_gtf_feature_type	    = 'transcript'
    features_gtf_table_first_field  = 'gene_id'

    // Affy-specific options
    affy_cel_files_archive   = null
    affy_file_name_col       = 'file'
    affy_background          = true
    affy_bgversion           = 2
    affy_destructive         = false
    affy_cdfname             = null
    affy_rm_mask             = false
    affy_rm_outliers         = false
    affy_rm_extra            = false
    affy_build_annotation    = true

    // Proteus-specific options
    proteus_measurecol_prefix = 'LFQ intensity'
    proteus_norm_function     = 'normalizeMedian'
    proteus_plotsd_method     = 'violin'
    proteus_plotmv_loess      =  true
    proteus_palette_name      = 'Set1'

    // Filtering options
    filtering_min_samples           = 1.0
    filtering_min_abundance         = 1.0
    filtering_min_proportion        = null
    filtering_grouping_var          = null
    filtering_min_proportion_not_na = 0.5
    filtering_min_samples_not_na    = null

    // Exploratory options
    exploratory_main_variable      = 'auto_pca'
    exploratory_clustering_method  = "ward.D2"
    exploratory_cor_method         = "spearman"
    exploratory_n_features         = 500
    exploratory_whisker_distance   = 1.5
    exploratory_mad_threshold      = -5
    exploratory_assay_names        = "raw,normalised,variance_stabilised"
    exploratory_final_assay        = "variance_stabilised"
    exploratory_log2_assays        = 'raw,normalised'
    exploratory_palette_name       = 'Set1'

    // Differential options
    differential_file_suffix                = null
    differential_feature_id_column          = "gene_id"
    differential_feature_name_column        = "gene_name"
    differential_fc_column                  = "log2FoldChange"
    differential_pval_column                = "pvalue"
    differential_qval_column                = "padj"
    differential_min_fold_change            = 2.0
    differential_max_pval                   = 1.0
    differential_max_qval                   = 0.05
    differential_foldchanges_logged         = true
    differential_palette_name               = 'Set1'
    differential_subset_to_contrast_samples = false

    // DESeq2-specific options
    deseq2_test                       = "Wald"
    deseq2_fit_type                   = "parametric"
    deseq2_sf_type                    = 'ratio'
    deseq2_min_replicates_for_replace = 7
    deseq2_use_t                      = false
    deseq2_lfc_threshold              = 0
    deseq2_alt_hypothesis             = 'greaterAbs'
    deseq2_independent_filtering      = true
    deseq2_p_adjust_method            = 'BH'
    deseq2_alpha                      = 0.1
    deseq2_minmu                      = 0.5
    deseq2_vs_method                  = 'vst' // 'rlog', 'vst', or 'rlog,vst'
    deseq2_shrink_lfc                 = true
    deseq2_cores                      = 1
    deseq2_vs_blind                   = true
    deseq2_vst_nsub                   = 1000

    // Limma-specific options
    limma_ndups             = null
    limma_spacing           = null
    limma_block             = null
    limma_correlation       = null
    limma_method            = 'ls'
    limma_proportion        = 0.01
    limma_stdev_coef_lim    = '0.1,4'
    limma_trend             = false
    limma_robust            = false
    limma_winsor_tail_p     = '0.05,0.1'
    limma_adjust_method     = "BH"
    limma_p_value           = 1.0
    limma_lfc               = 0
    limma_confint           = false

    // GSEA options
    gsea_run             = false

    gsea_nperm                  = 1000
    gsea_permute                = 'phenotype'
    gsea_scoring_scheme         = 'weighted'
    gsea_metric                 = 'Signal2Noise'
    gsea_sort                   = 'real'
    gsea_order                  = 'descending'
    gsea_set_max                = 500
    gsea_set_min                = 15

    gsea_norm                   = 'meandiv'
    gsea_rnd_type               = 'no_balance'
    gsea_make_sets              = true
    gsea_median                 = false
    gsea_num                    = 100
    gsea_plot_top_x             = 20
    gsea_rnd_seed               = 'timestamp'
    gsea_save_rnd_lists         = false
    gsea_zip_report             = false

    // gprofiler2 options
    gprofiler2_run                          = false
    gprofiler2_organism                     = null
    gprofiler2_significant                  = true
    gprofiler2_measure_underrepresentation  = false
    gprofiler2_correction_method            = 'gSCS'
    gprofiler2_sources                      = null
    gprofiler2_evcodes                      = false
    gprofiler2_max_qval                     = 0.05
    gprofiler2_token                        = null
    gprofiler2_background_file              = 'auto'
    gprofiler2_background_column            = null
    gprofiler2_domain_scope                 = 'annotated'
    gprofiler2_min_diff                     = 1
    gprofiler2_palette_name                 = 'Blues'

    // ShinyNGS
    shinyngs_build_app              = true

    // Note: for shinyapps deployment, in addition to setting these values,
    // SHINYAPPS_TOKEN and SHINYAPPS_SECRET must be available to the
    // environment, probably via Nextflow secrets
    shinyngs_deploy_to_shinyapps_io = false
    shinyngs_shinyapps_account      = null
    shinyngs_shinyapps_app_name     = null

    // Gene set options
    gene_sets_files                 = null

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

    // 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
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'

    // 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

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '128.GB'
    max_cpus                   = 16
    max_time                   = '240.h'

    // Schema validation default options
    validationFailUnrecognisedParams = false
    validationLenientMode            = false
    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
    validationShowHiddenParams       = false
    validate_params                  = true

}

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

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load nf-core/differentialabundance custom profiles from different institutions.
try {
    includeConfig "${params.custom_config_base}/pipeline/differentialabundance.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config/differentialabundance profiles: ${params.custom_config_base}/pipeline/differentialabundance.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', 'defaults']
        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
    }
    test      { includeConfig 'conf/test.config'      }
    test_nogtf { includeConfig 'conf/test_nogtf.config' }
    test_full { includeConfig 'conf/test_full.config' }
    affy { includeConfig 'conf/affy.config' }
    maxquant { includeConfig 'conf/maxquant.config' }
    rnaseq { includeConfig 'conf/rnaseq.config' }
    soft {includeConfig 'conf/soft.config'}
    test_affy { includeConfig 'conf/test_affy.config' }
    test_maxquant { includeConfig 'conf/test_maxquant.config' }
    test_soft {includeConfig 'conf/test_soft.config' }
    test_experimental {includeConfig 'conf/test_experimental.config' }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / 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'

// Nextflow plugins
plugins {
    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}
// 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"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'nf-core/differentialabundance'
    author          = 'Oskar Wacker, Jonathan Manning'
    homePage        = 'https://github.com/nf-core/differentialabundance'
    description     = 'Differential abundance analysis'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.10.0'
    version         = '1.6.0dev'
    doi             = '10.5281/zenodo.7568000'
}

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

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}