nextflow.config

/*****************************
 BARtab pipeline configuration
 *****************************/
manifest {
  name = 'DaneVass/BARtab'
  author = 'Dane Vassiliadis, Henrietta Holze'
  homePage = 'www.github.com/DaneVass/BARtab'
  description = 'A Nextflow pipeline to tabulate synthetic barcode counts from NGS data.'
  mainScript = 'BARtab.nf'
  version = '1.4.0'
  defaultBranch = 'main'
}

// Default pipeline params
params {
  help                 = false
  indir                = null
  outdir               = "./"
  input_type           = "fastq"
  pipeline             = null
  mode                 = null
  ref                  = null
  mergeoverlap         = 10
  minqual              = 20
  pctqual              = 80
  complexity_threshold = 0
  constants            = "up"
  upconstant           = "CGATTGACTA" // SPLINTR 1st gen upstream constant region
  downconstant         = "TGCTAATGCG" // SPLINTR 1st gen downstream constant region
  up_coverage          = 3
  down_coverage        = 3
  constantmismatches   = 0.1
  min_readlength       = 20
  barcode_length       = null
  alnmismatches        = 2
  cluster_unmapped     = false
  cb_umi_pattern       = "CCCCCCCCCCCCCCCCNNNNNNNNNNNN"
  cellnumber           = null
  whitelist_indir      = null
  umi_dist             = 1
  cluster_distance     = 3
  cluster_ratio        = 3
  umi_count_filter     = 1
  umi_fraction_filter  = 0.3
  max_cpus             = 6
  max_memory           = "14.GB"
  max_time             = "40.h"
  email                = null
}

executor {
  queueSize = 100
  submitRateLimit = '10 sec'
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
  // load profiles
  // standard    { includeConfig 'conf/standard.config'    }
  slurm       { includeConfig 'conf/slurm.config'       }
  lsf         { includeConfig 'conf/lsf.config'         }
  conda       { includeConfig 'conf/conda.config'       }
  docker      { includeConfig 'conf/docker.config'      }
  singularity { includeConfig 'conf/singularity.config' }

  // test profiles
  test_SE           { includeConfig 'conf/test_SE.config'                   }
  test_PE           { includeConfig 'conf/test_PE.config'                   }
  test_SE_ref_free  { includeConfig 'conf/test_SE_ref_free.config'          }
  test_sc           { includeConfig 'conf/test_sc.config'                   }
  test_sc_unmapped  { includeConfig 'conf/test_sc_cluster_unmapped.config'  }
  test_sc_bam       { includeConfig 'conf/test_sc_bam.config'               }
  test_sc_saw_fastq { includeConfig 'conf/test_sc_saw_fastq.config'         }
  test_sc_ref_free  { includeConfig 'conf/test_sc_ref_free.config'          }
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// from nf-core
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// Function to ensure that resource requirements don't go beyond (nf-core)
// 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
        }
    }
}