nextflow.config

params {

    help = false
  
    dragen_tmp = "/staging/tmp"
    assembly = "hg38"
    vep_assembly = "GRCh38"
    kit = false
    no_ml = true

    email = false
    sender = false
    plaintext_email = false
    skip_multiqc = false

    trio = false
    run_name = false
    outdir = "results"
    joint_calling = true
    exome = false
    bed = false
    check = true

    phase = false
    targets = null
    baits = null
    bed = null
    cnv_panel = null

    dragen_unit_cost = 0.13

    multiqc = false
    
    cnv = true
    sv = true
    clingen = false
    hla = false
    pgx = false
    trim = true

    summary = false
    min_mapq = 10

    kill = false
    panel = false
    all_panels = false
    panel_intervals = false
    panel_coverage = 10

    expansion_hunter = true

    interval_padding = 15

    vep = true
    dbnsfp_db = false
    dbnsfp_fields = "DANN_score,M-CAP_pred,REVEL_score"
    dbscsnv_db = false
    cadd_snps = false
    cadd_indels = false

    vep_cache_dir = false
    vep_plugin_dir = false

    logo = "${baseDir}/assets/ikmblogo.png"

    max_cpus = 24
    max_memory = 250.GB
    max_time = 120.h
  
}

container = "ikmb/dragen-variant-calling:1.1"

manifest {
  version = "1.1.1"
  description = "Dragen Variant Calling Pipeline"
  author = "Marc P. Hoeppner"
  homePage = "https://github.com/ikmb/dragen-variant-calling"
  nextflowVersion = "20.10.0"
}

timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/dragen-variant-calling_timeline.html"
}
report {
    enabled = true
    file = "${params.outdir}/pipeline_info/dragen-variant-calling_report.html"
}
trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/dragen-variant-calling_trace.txt"
}
dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/dragen-variant-calling_dag.svg"
}

profiles {
    standard {
      includeConfig 'conf/diagnostic.config'
      includeConfig 'conf/base.config'
      includeConfig 'conf/resources.config'
      includeConfig 'conf/references.config'
    }
    test {
      includeConfig 'conf/test.config'
    }

    test_trio {
      includeConfig 'conf/test_trio.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
    }
  }
}