config for nf-core/methylseq

bismark.config

/*
 * -------------------------------------------------
 *  Base Nextflow config file
 * -------------------------------------------------
 * This file contains basic process requirement setup
 * It DOES NOT contain any config for cluster, so will run
 * in default mode by itself. It should be used with
 * the max_memory, max_cpus and max_time params for
 * customising hardware limits
 */

process {

  // adding deep cache to help with resume
  cache = 'deep'

  withName:fastqc {
    cpus = 4
    memory = 64.GB
    time = 6.h
  }
  withName:bismark_methXtract {
    time = 96.h
  }

}

// Defaults config params, may be overwritten by later configs
params {
  resume = true
  igenomes_base = 's3://ngi-igenomes/igenomes/'
  genome = 'GRCh37'

  bismark_index = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
  fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"

  reads = 'data/*{1,2}.fastq.gz'
  saveReference = true
  saveTrimmed = true
}

docker {
  enabled = true
}