nextflow.config

// Please do not change the order of the numbered sections!
// The expected order is: 1. Parameters - 2. Profiles - 3. Process -  4. Executor

// There is a high chance it would break the configuration of 'profiles'

// 1. Parameters

// NOTE: 
// Initialise the values of the params to the preferred default value or to false

// biograph full_pipeline --biograph my.bg --ref hs37d5/ \
//  --reads /path/to/my_reads.bam \
//  --model /path/to/biograph_model-6.0.5.ml \
//  --tmp /path/to/large/tmp/

params {
    // input options
    input_tsv = false
    reference_tar_gz = false
    bedfile = 'NO_FILE'
    
    outdir = 'results'

    // report_dir is:
    // - the folder from the container that includes the scripts for NF <= v20.01 (bin)
    // - the ${projectDir}/bin folder of the root of the repo with the scripts for NF >= v20.10
    report_dir = '/opt/bin/'

    // when set to true, prints help and exits
    help = false
    
    // container for all processes, excluding those defined with 'withName' (see example below)
    container = 'quay.io/lifebitai/ubuntu:18.10'

    // process resources defaults
    cpus = 2
    memory = 4.GB
    disk = '120.GB'
    
    biograph_cpus = 20
    biograph_memory = 120.GB
    biograph_maxmem = 120
    biograph_error_msg = 'Segmentation Fault'

    // max resources limits defaults
    max_cpus = 128
    max_memory = 120.GB
    max_time = 8.h
    
    // execution related defaults
    config = 'conf/standard.config'
    echo = true
    errorStrategy = 'ignore'
    maxRetries = 5
    maxForks = 200
    queueSize = 10
    executor = false

    // google-lifesciences
    gls_bootDiskSize = '50.GB'
    gls_preemptible = true
    zone = 'us-east1-b'
    network = 'default'
    subnetwork = 'default'
}


// 2. Profiles


// Do not update the order because the values set in params scope will not be overwritten
// Do not attempt to simplify to 
// includeConfig params.config 
// outside of profiles scope, it will fail to update the values of the params
profiles {
    standard {includeConfig params.config}
    docker { docker.enabled = true }
    base {includeConfig 'conf/base.config'}
    google {includeConfig 'conf/google.config'}
    test {includeConfig 'conf/test.config'}
    local {includeConfig 'conf/test.config'}
}

// 3. Process

// Do not change order of block, must follow after profiles scope (last section that updates params)
process {
    echo = params.echo
    cpus = params.cpus
    memory = params.memory
    maxRetries = params.maxRetries
    maxForks = params.maxForks
    container = params.container
    errorStrategy = params.errorStrategy
  
    // If your pipeline doesn't include a process named 'step_1', update the name to match your process of choice or delete this block
    withName: step_1 {
        cpus = params.biograph_cpus
        memory = params.biograph_memory
        echo = true
    }
    withName: biograph {
        maxForks = params.maxForks
        disk = '200.GB'
        cpus = params.biograph_cpus
        memory = params.biograph_memory
        echo = true
        container = 'spiralgenetics/biograph:biograph-7.0.0'
    }
    
}

// 4. Executor

executor {
    name = params.executor
    queueSize = params.queueSize
}

timeline {
  enabled = true
  file = "${params.outdir}/pipeline_info/execution_timeline.html"
}

report {
  enabled = true
  file = "${params.outdir}/pipeline_info/execution_report.html"
}

trace {
  enabled = true
  file = "${params.outdir}/pipeline_info/execution_trace.txt"
  fields = 'task_id,process,tag,name,status,exit,cpus,%cpu,memory,%mem,rss,vmem,peak_rss,peak_vmem,disk,wchar,time,realtime,attempt,duration'
}