uppmax.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  Nextflow config file for UPPMAX (milou / irma)
 * -------------------------------------------------
 * Imported under the default 'standard' Nextflow
 * profile in nextflow.config
 */


process {
  executor = 'slurm'
  clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }

  // Environment modules and resource requirements
  $makeBowtieIndex {
    module = ['bioinfo-tools', 'bowtie/1.2.0', 'Fastx/0.0.14']
  }
  $fastqc {
    module = ['bioinfo-tools', 'FastQC/0.7.2']
  }
  $trim_galore {
    module = ['bioinfo-tools', 'TrimGalore/0.4.1', 'FastQC/0.7.2']
  }
  $insertsize {
  }
  $bowtie_miRBase_mature {
    module = ['bioinfo-tools', 'bowtie/1.2.0', 'samtools/1.5']
  }
  $bowtie_miRBase_hairpin {
    module = ['bioinfo-tools', 'bowtie/1.2.0', 'samtools/1.5']
  }
  $miRBasePostAlignment {
    module = ['bioinfo-tools', 'samtools/1.5']
  }
  $edgeR_miRBase {
    module = ['bioinfo-tools', 'R/3.2.3']
  }
  $bowtie2 {
    module = ['bioinfo-tools', 'bowtie2/2.3.2', 'samtools/1.5']
  }
  $bowtie2_unmapped {
    module = ['bioinfo-tools', 'samtools/1.5']
  }
  $ngi_visualizations {
  }
  $get_software_versions {
    module = ['bioinfo-tools', 'bowtie/1.2.0', 'Fastx/0.0.14', 'TrimGalore/0.4.1', 'FastQC/0.7.2', 'samtools/1.5', 'bowtie2/2.3.2', 'MultiQC/1.2']
  }
  // NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
  // if you have your own installation of MultiQC outside of the environment module system.
  // eg: Add the line: process.$multiqc.module = []
  $multiqc {
    module = ['bioinfo-tools', 'MultiQC/1.2']
  }
}

params {
  clusterOptions = false
  rlocation = "$HOME/R/nxtflow_libs/"
  // Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
  //   --clusterOptions "-C mem512GB" --max_memory "512GB"
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h
  // illumina iGenomes reference file paths on UPPMAX
  igenomes_base = '/sw/data/uppnex/igenomes/'
}