NGI-ChIPseq/nextflow.config at master · SciLifeLab/NGI-ChIPseq · GitHub

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/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  NGI-ChIPseq 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.
 */


// Variable to specify the docker / singularity image tag to use
// Picks up on use of -r 1.3 in nextflow command
wf_container = { "scilifelab/ngi-chipseq:${workflow.revision ? workflow.revision : 'latest'}" }

// Global default params, used in configs
params {
    outdir = './results'
    igenomes_base = "./iGenomes"
}

profiles {

  standard {
    includeConfig 'conf/base.config'
  }
  uppmax {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax.config'
    includeConfig 'conf/igenomes.config'
  }
  uppmax_modules {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax.config'
    includeConfig 'conf/uppmax-modules.config'
    includeConfig 'conf/igenomes.config'
  }
  uppmax_devel {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax.config'
    includeConfig 'conf/uppmax-devel.config'
    includeConfig 'conf/igenomes.config'
  }
  docker {
    includeConfig 'conf/docker.config'
  }
  testing {
    includeConfig 'conf/testing.config'
  }
  aws {
    includeConfig 'conf/base.config'
    includeConfig 'conf/aws.config'
    includeConfig 'conf/igenomes.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']

timeline {
  enabled = true
  file = "${params.outdir}/NGI-ChIPseq_timeline.html"
}
trace {
  enabled = true
  file = "${params.outdir}/NGI-ChIPseq_trace.txt"
}

manifest {
  homePage = 'https://github.com/SciLifeLab/NGI-ChIPseq'
  description = 'NGI-ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.'
}

// 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 )
  }
}