nextflow.config

includeConfig 'VERSION'
/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  scsHi-C Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

profiles {
  cluster {
    includeConfig 'conf/cluster.config'
  }
  local {
    includeConfig 'conf/local.config'
  }
  none {
    // Don't load any config (for use with custom home configs)
  }
}

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


manifest {
    homePage = 'https://christophlanger.com'
    name = 'scshic-nf'
    mainScript = 'main.nf'
    nextflowVersion = '>=20.01.0'
    description = 'scsHi-C preprocessing nextflow pipline (IMBA - Gerlichlab)'
}


// Function to ensure that resource requirements don't go beyond a maximum limit
def check_max(obj, type) {
  if(type == 'memory'){
    if(obj.compareTo(params.max_memory) == 1)
      return params.max_memory
    else
      return obj
  } else if(type == 'time'){
    if(obj.compareTo(params.max_time) == 1)
      return params.max_time
    else
      return obj
  } else if(type == 'cpus'){
    return Math.min( obj, params.max_cpus )
  }
}