nextflow.config

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

// Global default params, used in configs
params {

    // Input options
    input                      = null
    method                     = 'HiCAR'
    anchor_peaks               = null

    // References
    genome                     = null
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    igenomes_ignore            = false
    ucscname                   = null
    mappability                = null
    blacklist                  = null
    publish_genome             = false
    publish_mappability        = false

    // Enzyme
    enzyme                     = 'CviQI'
    restriction_sites          = '^TAC'
    restriction_sites_cut_off  = 0.5

    // ATAC peak calling
    shiftsize                  = -75
    smooth_window              = 150
    qval_thresh                = 0.01

    // Pipeline controler
    // trim reads; !important
    skip_cutadapt              = false
    cutadapt_5end              = '^TAC'
    resample_pairs             = false
    // caller controls
    skip_compartments          = false
    skip_tads                  = false
    skip_interactions          = false
    do_apa                     = false
    call_high_peak             = false
    // Options: QC
    skip_fastqc                = false
    skip_plot_profile          = false
    skip_igv                   = false
    skip_multiqc               = false
    skip_peak_qc               = false
    // Options: visualization
    skip_trackhub              = false
    create_virtual_4c          = false
    skip_circos                = false
    create_maps_signal         = false
    // Options: downstream additional
    skip_diff_analysis         = false
    skip_peak_annotation       = false
    do_tfea                    = false

    //
    // Dowstream analysis
    //
    // callers
    interactions_tool          = 'maps'
    tad_tool                   = 'hicexplorer'
    compartments_tool          = 'cooltools'
    apa_tool                   = 'hicexplorer'
    da_tool                    = 'diffhic'
    v4c_tool                   = 'hicexplorer'
    tfea_tool                  = 'homer'
    // Options: resolutions
    res_tads                   = 10000
    res_compartments           = 100000
    // Options: apa 1D peaks
    apa_peak                   = null
    apa_format                 = 'pdf'
    // Options: Differential analysis
    enrichment_fdr             = 0.05
    // Options: v4c
    v4c_max_events             = 25

    // MAPS bins, MAPS resolution
    cool_bin                   = '5000_10000'
    maps_digest_file           = null
    maps_cutoff_counts         = 12
    maps_cutoff_fold_change    = 2
    maps_cutoff_fdr            = 2
    maps_filter                = 'None'
    maps_model                 = 'pospoisson'
    maps_3d_ext                = 'sig3Dinteractions.pe.txt'

    // HiCDCPlus
    hicdcplus_cutoff_fdr       = 0.05

    // peakachu
    peakachu_pretrained_url    = 'http://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.'

    // HiCExplorer
    peak_interactions_threshold  = 2

    // Juicer
    juicer_norm_method         = 'SCALE'

    // R1 peak calling
    r1_pval_thresh             = 0.1

    // HiPeak calling
    remove_dup                 = false
    snow_type                  = "SOCK"
    peak_pair_block            = 1e8
    min_counts_per_loop        = 1


    // 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                   = null
    help                       = false
    version                    = false

    // 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                 = '240.GB'
    max_cpus                   = 16
    max_time                   = '240.h'

    // Juicer Java paramaters
    juicer_tools_jar           = 'https://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jar'
    hic_tools_jar              = 'https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar'

    // File namespace
    long_bedpe_postfix         = 'long.bedpe'
    short_bed_postfix          = 'shrt.vip.bed'

    // Schema validation default options
    validationFailUnrecognisedParams = false
    validationLenientMode            = false
    validationSchemaIgnoreParams     = 'genomes'
    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/hicar custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
//   includeConfig "${params.custom_config_base}/pipeline/hicar.config"
// } catch (Exception e) {
//   System.err.println("WARNING: Could not load nf-core/config/hicar profiles: ${params.custom_config_base}/pipeline/hicar.config")
// }
profiles {
    debug {
        dumpHashes             = true
        process.beforeScript   = 'echo $HOSTNAME'
        cleanup                = false
    }
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        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
        docker.userEmulation   = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    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
        conda.enabled          = false
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    gitpod {
        executor.name          = 'local'
        executor.cpus          = 16
        executor.memory        = 60.GB
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
    test_hipeak   { includeConfig 'conf/test_hipeak.config'   }
    test_multi    { includeConfig 'conf/test_multi.config'    }
    test_hichip   { includeConfig 'conf/test_hichip.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' // 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']

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/hicar'
    author          = """Jianhong Ou, Yu Xiang, Yarui Diao"""
    homePage        = 'https://github.com/nf-core/hicar'
    description     = """This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts."""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '2.0.0'
    doi             = '10.1016/j.molcel.2022.01.023'
}

// 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
        }
    }
}