nextflow.config

manifest {
  name = 'ViralClust'
  mainScript = 'viralclust.nf'
  author = 'Kevin Lamkiewicz'
}

// default parameters
params {
  max_cores = Runtime.runtime.availableProcessors()
  cores = '2'
  memory = '16.GB'
  help = false
  hdbscan_help = false
  sumaclust_help = false
  vclust_help = false
  cdhit_help = false
  mmseqs_help = false
  profile = false

  // input
  fasta = ''
  goi = ''

  // output
  output = 'viralclust_results'
  sort_output = '00-positive_sorted'
  nr_output = '01-non_redundant'
  cdhit_output = '02-cdhit'
  hdbscan_output = '03-hdbscan'
  sumaclust_output = '04-sumaclust'
  vclust_output = '05-vclust'
  mmseqs_output = '06-mmseqs'
  mafft_output = '07-mafft'
  fasttree_output = '08-fasttree'
  css_output = '08-fasttree'
  nwdisplay_output = '08-fasttree'
  eval_output = '09-evaluation'
  summary_output = 'summary'


  // modules on/off
  cdhit_off = false
  hdbscan_off = false
  sumaclust_off = false
  vclust_off = false
  mmseqs_off = false


  // parameters
  eval = false
  ncbi = false
  sort_off = false
  dedup_off = false
  update_ncbi = false
  cdhit_params = '-c 0.9'
  hdbscan_params = '-k 7'
  sumaclust_params = '-t 0.9'
  vclust_params = '--id 0.9'
  mmseqs_params = '--min-seq-id 0.9'

  // location for databases
  permanentCacheDir = "${projectDir}/data"

  // location for storing the conda environments
  condaCacheDir = "${projectDir}/conda"

  // optional configurations
  workdir = "/tmp/nextflow-work-$USER"
  cloudDatabase = false
  cachedir = false
}

profiles {
  local {
    params.cloudProcess = false
    params.cloudDatabase = false
    includeConfig 'configs/local.config'
    permanentCacheDir = 'data'
  }

  conda {
    conda {
      useMicromamba = true
      enabled = true
      params.cloudProcess = false
      params.cloudDatabase = false
      conda.cacheDir = params.condaCacheDir
    }
    includeConfig 'configs/conda.config'
  }

  mamba {
    conda {
      enabled = true
      params.cloudProcess = false
      params.cloudDatabase = false
      conda.cacheDir = params.condaCacheDir
      useMamba = true
    }
    includeConfig 'configs/conda.config'
  }


  // predefined combinations
  // local execution with conda
  standard {
    conda {
      enabled = true
    }
    conda.cacheDir = params.condaCacheDir
    permanentCacheDir = 'data'
    process.cache = 'lenient'
    includeConfig 'configs/local.config'
    includeConfig 'configs/conda.config'
  }

}