nextflow.config

/*
 * -------------------------------------------------
 *  nf-core/smrnaseq 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.
 */

params {

  version = '0.2dev' // Pipeline version
  nf_required_version = '0.30.2' // Minimum version of nextflow required
  container = 'nfcore/smrnaseq:latest' // Container slug. Stable releases should specify release tag!!

  // Pipeline options
  params.name = false
  params.project = false
  params.genome = false
  params.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
  params.bt2index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
  params.bt2indices = null
  params.mature = params.genome ? params.genomes[ params.genome ].mature ?: false : false
  params.hairpin = params.genome ? params.genomes[ params.genome ].hairpin ?: false : false
  params.saveReference = false
  params.reads = "data/*.fastq.gz"
  params.readPaths = null
  params.outdir = './results'
  multiqc_config = "$baseDir/conf/multiqc_config.yaml"
  params.email = false
  params.plaintext_email = false

  // Custom trimming options
  params.length = 18
  params.clip_R1 = 0
  params.three_prime_clip_R1 = 0
}

profiles {

  standard {
    includeConfig 'conf/base.config'
    includeConfig 'conf/igenomes.config'
  }
  conda { process.conda = "$baseDir/environment.yml" }
  docker { docker.enabled = true }
  singularity { singularity.enabled = true }
  uppmax {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax.config'
    includeConfig 'conf/igenomes.config'
  }
  test {
    includeConfig 'conf/base.config'
    includeConfig 'conf/test.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 = "${params.outdir}/pipeline_info/smRNAseq_timeline.html"
}
report {
  enabled = true
  file = "${params.outdir}/pipeline_info/smRNAseq_report.html"
}
trace {
  enabled = true
  file = "${params.outdir}/pipeline_info/smRNAseq_trace.txt"
}
dag {
  enabled = true
  file = "${params.outdir}/pipeline_info/smRNAseq_dag.svg"
}

manifest {
  homePage = 'https://github.com/nf-core/smrnaseq'
  description = 'Nextflow small RNA sequencing analysis pipeline.'
  mainScript = 'main.nf'
}

// 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
    }
  }
}