merge_fastq/nextflow.config at master · ameynert/merge_fastq · GitHub

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/*
 * -------------------------------------------------
 *  nf-core/merge_fastq 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.
 */

// Global default params, used in configs
params {
  help = false
  inputdir = "fastq_files"
  outdir = './merged_fastq_files'
  suffix = ''
  toremove = ''
  tracedir = "${params.outdir}/pipeline_info"
  clusterOptions = false
}

profiles {

  conda {
    process.conda = "$baseDir/environment.yml"
  }

  ultra {
    includeConfig 'conf/ultra.config'
  }

  eddie {
    includeConfig 'conf/eddie.config'
  }

  legion {
    includeConfig 'conf/legion.config'
  }
  myriad {
    includeConfig 'conf/myriad.config'
  }

}

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

timeline {
  enabled = false
  file = "${params.tracedir}/merge_fastq_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/merge_fastq_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/merge_fastq_trace.txt"
}
dag {
  enabled = false
  file = "${params.tracedir}/merge_fastq_dag.svg"
}

manifest {
  name = 'nf-core/merge_fastq'
  author = 'LC, based on the \'merge_and_rename_NGI_fastq_files.py\' standalone-script from https://github.com/SciLifeLab/standalone_scripts'
  homePage = 'https://github.com/UCL-BLIC/merge_fastq'
  description = 'Merge FastQ files'
  mainScript = 'main.nf'
  nextflowVersion = '>=0.32.0'
  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
    }
  }
}