nextflow.config

manifest {
    author = 'Mahsa Mousavi-Derazmahalleh'
    name = 'eDNAFlow' 
    homePage = 'http://github.com/mahsa-mousavi/eDNAFlow'
    description = 'Pipeline identifies Zotus using USEARCH unoise3'
    mainScript = 'eDNAFlow.nf'
    version = '1.0.0'
}


resume = true


trace {
  
  fields = 'name,hash,status,exit,realtime,submit,%cpu,%mem'
}


/*
 * Define the pipeline parameters
 * Each of these parameters can be specified at command line (e.g. --barcode 'x.txt'); if none specified the below will be set as default 
 */

params {
reads   = "*_{R1,R2}.fastq"
barcode = "*_bc.txt"
minQuality = "20"
minAlignLeng = "12"
minLen = "50"
primer_mismatch = "2"
minsize = "8"
maxTarSeq = "10"
perc_identity = "95"
evalue = "1e-3"
qcov = "100"
lulu = "lulu.R"
mode = "usearch32"  
usearch64 = ""   
blast_db = ""
custom_db = ""
blast_task = "blastn"
publish_dir_mode = "symlink" 
bindDir = ""
singularityDir = ""

lca_script = "LCA_taxonomyAssignment_scripts/runAssign_collapsedTaxonomy.py"
zotuTable = ""
blastFile = ""
lca_qcov = "100"
lca_pid = "97"
lca_diff = "1"
lca_output = "lca_taxAssigned_results"

minMatch_lulu="84"

test = false
help = false

// 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
// move default values for singularity and process there and then enable
includeConfig 'conf/base.config'

// Load test parameters if required
if (params.test) {
  includeConfig 'conf/initialTest.config'
}

// Load profiles from conf/profiles.config
profiles {
  includeConfig 'conf/profiles.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
    }
  }
}