nextflow.config

/*
 * -------------------------------------------------
 *  nf-core/genebygenebact Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

// Global default params, used in configs
params {

  // Workflow flags

  // Options: Generic

  //input = './samplesheet.csv'
  input = ''
  save_fasta_assemblies = false

  schema = ''
  reference_alleles = ''
  st_profile = ''


  // Options: SRA download

  save_sra_fastq = false
  skip_sra_download = false

  // Options: NCBI assembly download

  save_ncbi_assembly_fasta = false
  skip_ncbi_assembly_download = false


  // Options: Schema download

  api = ''
  organism_id = ''
  schema_database = ''
  schema_type = ''
  skip_get_schema = true
  skip_get_profile = true


  // Options: Reference genomes

  genome = false
  fasta = ''
  gff = ''
  save_reference = false


  // Options: Quality Control

  skip_fastqc = false
  skip_multiqc = false


  // Options: Read Trimming

  cut_mean_quality = 30
  qualified_quality_phred = 30
  unqualified_percent_limit = 10
  min_trimming_length = 50
  skip_fastp_trimming = false
  save_trimmed = false


  // Options: De novo assembly

  skip_unicycler_assembly = false
  skip_quast = false


  // Options: Analyze Schema

  remove_subsets = false
  remove_duplicates = false
  remove_nocds = false
  new_schema = false
  skip_taranis_analyze_schema = true


  // Options: Reference Allele(s)

  evalue_ref = 0.001
  perc_identity_ref = 90
  reward_ref = 1
  penalty_ref = -2
  gap_open_ref = 1
  gap_extend_ref = 1
  num_threads_ref = 1
  skip_taranis_reference_alleles = false


  // Options: Allele Calling

  percentlength = 'SD'
  coverage = 50
  evalue_call = 0.001
  perc_identity_ref_call = 90
  perc_identity_loc_call = 90
  reward_call = 1
  penalty_call = -2
  gapopen_call = 1
  gapextend_call = 1
  max_target_seqs_call = 10
  max_hsps_call = 10
  num_threads_call = 1
  flanking_nts = 100
  update_schema = true
  st_profile = ''
  skip_taranis_allele_calling = false


  // Options: Distance Matrix

  alleles_matrix = ''
  locus_missing_threshold = 100
  sample_missing_threshold = 100
  paralog_filter = true
  lnf_filter = true
  plot_filter = true
  skip_taranis_distance_matrix = false


  // Boilerplate options
  outdir = './results'
  publish_dir_mode = 'copy'
  //name = false

  multiqc_config = false
  email = false
  email_on_fail = false
  max_multiqc_email_size = 25.MB
  plaintext_email = false
  monochrome_logs = false
  help = false
  //igenomes_base = 's3://ngi-igenomes/igenomes'
  tracedir = "${params.outdir}/pipeline_info"
  igenomes_ignore = false
  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames = false
  config_profile_name = null
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false
  validate_params = true
  show_hidden_params = false
  schema_ignore_params = 'genomes,input_paths'

  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h

}

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/genebygenebact:dev'

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

// Load nf-core custom profiles from different Institutions
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")
}

profiles {
  conda {
    docker.enabled = false
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    process.conda = "$projectDir/environment.yml"
  }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled = true
    singularity.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    // Avoid this error:
    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
    // once this is established and works well, nextflow might implement this behavior as new default.
    docker.runOptions = '-u \$(id -u):\$(id -g)'
  }
  singularity {
    docker.enabled = false
    singularity.enabled = true
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
    singularity.autoMounts = true
  }
  podman {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = true
    shifter.enabled = false
    charliecloud.enabled = false
  }
  shifter {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = true
    charliecloud.enabled = false
  }
  charliecloud {
    singularity.enabled = false
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = true
  }
  test { includeConfig 'conf/test.config' }
  test_full { includeConfig 'conf/test_full.config' }
}

// Load igenomes.config if required
//if (!params.igenomes_ignore) {
//  includeConfig 'conf/igenomes.config'
//}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
  PYTHONNOUSERSITE = 1
  R_PROFILE_USER = "/.Rprofile"
  R_ENVIRON_USER = "/.Renviron"
}

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

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

manifest {
  name = 'nf-core/genebygenebact'
  author = 'Esperanza López López'
  homePage = 'https://github.com/nf-core/genebygenebact'
  description = 'Gene-by-gene outbreaks analysis pipeline using cgMLST schemas.'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.04.0'
  version = '1.0dev'
}

// 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
    }
  }
}