nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    sanger-tol/genomenote Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options
    input                           = null
    binsize                         = 1000
    kmer_size                       = 31
    annotation_set                  = null
    
    // Metadata
    assembly                        = null
    biosample_wgs                   = null
    biosample_hic                   = null
    biosample_rna                   = null

    // Genome Notes 
    write_to_portal                 = false     
    genome_notes_api                = null
    note_template                   = null

    // HiGlass options
    upload_higlass_data             = false
    higlass_url                     = null
    higlass_upload_directory        = null
    higlass_data_project_dir        = null
    higlass_kubeconfig              = null
    higlass_deployment_name         = null
    higlass_namespace               = null

    // Database
    lineage_db                  = null
    // Taken from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz
    lineage_tax_ids             = "${projectDir}/assets/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt"

    // References
    fasta                       = null
    cool_order                  = null

    // Execution options
    use_work_dir_as_temp        = 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/genomenote"
    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'


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


profiles {
    cleanup { cleanup = true }
    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
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}


// 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"
    fields  = 'task_id,hash,native_id,process,tag,status,exit,cpus,memory,time,attempt,submit,start,complete,duration,%cpu,%mem,peak_rss,rchar,wchar'
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}

manifest {
    name            = 'sanger-tol/genomenote'
    author          = """@cibinsb, @muffato, @gq1, @priyanka-surana, @BethYates"""
    homePage        = 'https://github.com/sanger-tol/genomenote'
    description     = """Creating standarised genome assembly publications"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=22.10.1'
    version         = '2.1.1'
    doi             = '10.5281/zenodo.7949384'
}

// 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
        }
    }
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Increasing the number of CPUs often gives diminishing returns, so we increase it
    following a logarithm curve. Example:
        - 0 < value <= 1: start + step
        - 1 < value <= 2: start + 2*step
        - 2 < value <= 4: start + 3*step
        - 4 < value <= 8: start + 4*step
    In order to support re-runs, the step increase may be multiplied by the attempt
    number prior to calling this function.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// Modified logarithm function that doesn't return negative numbers
def positive_log(value, base) {
    if (value <= 1) {
        return 0
    } else {
        return Math.log(value)/Math.log(base)
    }
}

def log_increase_cpus(start, step, value, base) {
    return check_max(start + step * (1 + Math.ceil(positive_log(value, base))), 'cpus')
}