nextflow.config

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

// Global default params, used in configs
params {
    // Input options
    input                      = null
    seq_center                 = null
    fragment_size              = 200
    fingerprint_bins           = 500000
    read_length                = null

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

    // Options: Trimming
    clip_r1                    = null
    clip_r2                    = null
    three_prime_clip_r1        = null
    three_prime_clip_r2        = null
    trim_nextseq               = null
    skip_trimming              = false
    save_trimmed               = false

    // Options: Alignment
    aligner                    = 'bwa'
    bwa_min_score              = null
    keep_dups                  = false
    keep_multi_map             = false
    save_align_intermeds       = false
    save_unaligned             = false

    // Options: Peaks
    narrow_peak                = false
    broad_cutoff               = 0.1
    macs_fdr                   = null
    macs_pvalue                = null
    min_reps_consensus         = 1
    save_macs_pileup           = false
    skip_peak_qc               = false
    skip_peak_annotation       = false
    skip_consensus_peaks       = false

    // Options: DESeq2 QC
    deseq2_vst                 = true
    skip_deseq2_qc             = false

    // Options: QC
    skip_qc                    = false
    skip_fastqc                = false
    skip_picard_metrics        = false
    skip_preseq                = false
    skip_plot_profile          = false
    skip_plot_fingerprint      = false
    skip_spp                   = false
    skip_igv                   = false
    skip_multiqc               = false

    // Options: Config
    bamtools_filter_pe_config  = "$projectDir/assets/bamtools_filter_pe.json"
    bamtools_filter_se_config  = "$projectDir/assets/bamtools_filter_se.json"

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

    // Boilerplate options
    outdir                     = null
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    help                       = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes'
    enable_conda               = false

    // 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                 = '128.GB'
    max_cpus                   = 16
    max_time                   = '240.h'

}

// 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/chipseq 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/chipseq.config"
// } catch (Exception e) {
//   System.err.println("WARNING: Could not load nf-core/config/chipseq profiles: ${params.custom_config_base}/pipeline/chipseq.config")
// }

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        params.enable_conda    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    mamba {
        params.enable_conda    = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.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' }
}

// 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    = "${params.tracedir}/execution_timeline_${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"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'nf-core/chipseq'
    author          = 'Espinosa-Carrasco J, Patel H, Wang C, Ewels P'
    homePage        = 'https://github.com/nf-core/chipseq'
    description     = 'ChIP-seq peak-calling and differential analysis pipeline.'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version         = '2.0.0'
}

// 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
        }
    }
}