nextflow.config

manifest {
    author = 'Charles Plessy'
    description = 'Pairwise genome comparison'
    name = 'pairwiseGenomeComparison'
    homePage = 'https://github.com/oist/plessy_pairwiseGenomeComparison'
    nextflowVersion = '>=21.04.0'
    version = '8.6.0'
}

params {
// windowmasker
    with_windowmasker                 = false

// lastdb
    keepOriginalMask                  = false
    seed                              = 'YASS'

// lastal and last-train
    lastal_args                       = '-C2'   // from the LAST cookbook
    lastal_extra_args                 = '-D1e9' // args that are passed only to lastal
    lastal_params                     = false
    query                             = false  // Bypass --input with a single fasta file.
    m2m                               = false
    read_align                        = false
    lowmem                            = false

// last-split
    o2m                               = false
    last_split_args                   = ''
    last_split_mismap                 = '1e-5'

// dotplots
    skip_dotplot_m2m                  = false
    skip_dotplot_m2o                  = false
    skip_dotplot_o2m                  = false
    skip_dotplot_o2o                  = false
    dotplot_options                   = ''

// postmask
    postmask                          = false

// nf-core parameters
    enable_conda                      = false
    outdir                            = './results'
    publish_dir_mode                  = 'copy'
    singularity_pull_docker_container = false

// Mandatory parameters
    input                             = false
    target                            = false

// Other options
    targetName                        = ''
    one_to_one_only                   = false

// Load nf-core custom profiles from different Institutions
    custom_config_version             = 'master'
    custom_config_base                = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
}

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")
}

// https://nf-co.re/docs/usage/troubleshooting
// https://github.com/nf-core/rnaseq/blob/3643a94411b65f42bce5357c5015603099556ad9/nextflow.config#L190-L221
def check_max(obj, type) {
  if (type == 'memory') {
    if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
      return params.max_memory as nextflow.util.MemoryUnit
    else
      return obj
  } else if (type == 'time') {
    if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
      return params.max_time as nextflow.util.Duration
    else
      return obj
  } else if (type == 'cpus') {
    return Math.min( obj, params.max_cpus as int )
  }
}

process {
  withLabel:process_low {
    cpus = 2
    memory = 14.GB
    time =  6.h
  }
  withLabel:process_medium {
    cpus = 6
    memory = 42.GB
    time = 8.h
  }
  withLabel:process_high {
    cpus = 12
    memory = {check_max( 48.GB * Math.pow(2, (task.attempt - 1)), 'memory' ) }
    time = 10.h
  }
  withLabel:process_long {
    time = 20.h
  }
  withName:LAST_SPLIT {
    cpus = 2
    memory = 40.GB
    time = 8.h
  }
}

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

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

trace {
  enabled = true
  file = "$params.outdir/trace.tsv"
  fields = 'hash,duration,cpus,%cpu,memory,peak_rss,status,name'
}