nextflow.config

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

// Global default params, used in configs
params {

    // Choice of the workflow ('hicpro' or 'hicstuff')
    workflow = 'hicpro'

    // Input options
    input = null


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

    // Mapping
    split_fastq = false
    fastq_chunks_size = 20000000
    save_interaction_bam = false
    save_aligned_intermediates = false
    save_bam = false
    bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
    bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
    keep_dups = false
    keep_multi = false
    filter_pcr_picard = false
    min_mapq = 10

    //Save bam filtered by Picard
    save_bam_intermediates = false

    // Digestion Hi-C
    digestion = null
    ligation_site = null
    restriction_site = null
    digest {
      'hindiii'{
         restriction_site='A^AGCTT'
         ligation_site='AAGCTAGCTT'
      }
      'mboi' {
         restriction_site='^GATC'
         ligation_site='GATCGATC'
      }
      'dpnii' {
         restriction_site='^GATC'
         ligation_site='GATCGATC'
      }
      'arima' {
         restriction_site='^GATC,G^ANTC'
         ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
      }
    }

    min_restriction_fragment_size = 0
    max_restriction_fragment_size = 0
    min_insert_size = 0
    max_insert_size = 0
    save_pairs_intermediates = false
    save_pairs = false

    // Dnase Hi-C
    dnase = false
    min_cis_dist = 0

    // Contact maps
    save_raw_maps = false
    bin_size = '1000000'
    res_zoomify = null
    hicpro_maps = false
    ice_max_iter = 100
    ice_filter_low_count_perc = 0.02
    ice_filter_high_count_perc =  0
    ice_eps = 0.1

    // Downstream Analysis
    res_dist_decay = '250000'
    tads_caller = 'insulation'
    res_tads = '40000'
    res_compartments = '250000'

    // Workflow
    skip_maps = false
    skip_balancing = false
    skip_mcool = false
    skip_dist_decay = false
    skip_compartments = false
    skip_tads = false
    skip_multiqc = false
    skip_plot_matrix = false

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

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    hook_url                   = null
    help                       = false
    version                    = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes,digest,bin_size,res_dist_decay,res_tads,res_compartments'

    // Config options
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null


    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '64.GB'
    max_cpus                   = 16
    max_time                   = '240.h'

    // Hicstuff
    hicstuff_bwt2_align_opts = '--very-sensitive-local'
    hicstuff_min_size = 0
    hicstuff_circular = 'false'
    hicstuff_output_contigs = 'info_contigs.txt'
    hicstuff_output_frags = 'fragments_list.txt'
    hicstuff_frags_plot = 'false'
    hicstuff_frags_plot_path = 'frags_hist.pdf'
    hicstuff_valid_pairs = 'valid.pairs'
    hicstuff_valid_idx = 'valid_idx.pairs'
    hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
    hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
    hicstuff_plot_events = 'false'
    hicstuff_pie_plot = 'distrib'
    hicstuff_dist_plot = 'dist'
    hicstuff_centro_file = 'None'       //give absolute path or 'None'
    hicstuff_base = 1.1
    hicstuff_distance_out_file = 'distance_law.txt'
    hicstuff_rm_centro = 'None'         //string number (ex: '30') or 'None'
    hicstuff_distance_plot = 'false'
    hicstuff_distance_out_plot = 'plot_distance_law.pdf'
    hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
    hicstuff_read_len = 'None'
    hicstuff_tmp_dir = 'None'

    //Hicstuff optional modules
    filter_event = false
    distance_law = false
    filter_pcr = false

    //Hicstuff save intermediates files
    save_fragments = false

    //Cutsite
    cutsite_mode = 'for_vs_rev'
    cutsite_seed = 20
    save_digested = false
    cutsite = false

    //Parasplit
    parasplit_mode = 'all'
    parasplit_seed = 20

    //Iterative alignement
    iteralign = false
}

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

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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/hic 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/hic.config"
// } catch (Exception e) {
//   System.err.println("WARNING: Could not load nf-core/config/hic profiles: ${params.custom_config_base}/pipeline/hic.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.registry        = 'quay.io'
        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
        podman.registry        = 'quay.io'
        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
    }
    public_aws_ecr {
        includeConfig 'conf/public_aws_ecr.config'
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}


// 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']

// Set default registry for Docker and Podman independent of -profile
// Will not be used unless Docker / Podman are enabled
// Set to your registry if you have a mirror of containers
docker.registry = 'quay.io'
podman.registry = 'quay.io'

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
    fields  = "task_id,hash,name,status,exit,duration,submit,realtime,%cpu,%mem,peak_rss,peak_vmem,rchar,wchar"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'nf-core/hic'
    author          = """Nicolas Servant"""
    homePage        = 'https://github.com/nf-core/hic'
    description     = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=22.10.1'
    version         = '2.1.0'
    doi             = ''
}

// 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
        }
    }
}