RICO/nextflow.config at main · comprna/RICO · GitHub

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params {
  project   = 'jd21'
  storage   = 'gdata/jd21+scratch/jd21+gdata/xc17+gdata/qq78'
  container = '/g/data/xc17/zaka/containers/rico_2026.03.sif'

  minimap2 = 'minimap2'
  samtools = 'samtools'
  bedtools = 'bedtools'
  modkit   = 'modkit'

  species     = 'human'
  scg         = 2
  outdir      = "${projectDir}/results"
  samplesheet = "${projectDir}/samples.tsv"
}

singularity {
  enabled = true
  autoMounts = true
}

process {
  executor  = 'pbspro'
  project   = params.project
  storage   = params.storage
  module    = 'singularity'
  container = params.container

  withName: index {
    queue = 'normal'
    cpus = 1
    memory = '32 GB'
    time = '1h'
  }

  withName: align {
    queue = 'normal'
    cpus = 40
    memory = '128 GB'
    time = '48h'
  }

  withName: mean_cn {
    queue = 'normal'
    cpus = 4
    memory = '16 GB'
    time = '24h'
  }

  withName: mod_pileup {
    queue = 'normal'
    cpus = 24
    memory = '128 GB'
    time = '24h'
  }

  withName: cg_motifs {
    queue = 'normal'
    cpus = 1
    memory = '32 GB'
    time = '1h'
  }

  withName: mod_extract_read {
    queue = 'normal'
    cpus = 24
    memory = '128 GB'
    time = '12h'
  }
}