custom.config

//Change this file to your own custom values before running this pipeline!

params {
  //Software DB locations, UNCOMMENT AND CHANGE THEM:

  //metaphlan_db = "${baseDir}/databases/Metaphlan/4.0"
  //kraken2_db = "${baseDir}/databases/Kraken2/k2_viral_20210517"
  //humann_db = "${baseDir}/databases/Humann3/3.6" 
  //gtdbtk_reference = "${baseDir}/databases/GTDB-TK/release207_v2"

  //For host read removal list your host genomes as bowtie2 index in this named list with full path to the basename of the index:
	'genomes' {
		'human' {
      bowtie_index = false
      //bowtie_index = "${baseDir}/databases/human/GRCh38_noalt_decoy_as/GRCh38_noalt_decoy_as"
		}
	}

  // MAXIMUM PER PROCESS CONFIGS, CHANGE THEM TO YOUR HARDWARE SPECS
  max_memory = 100.GB
  max_cpus = 32
  max_time = 48.h
  
  //Scratch. Does your system support scratch? If not, leave it false
  scratch = false
}

//Enable Singularity as container software
singularity {
	enabled = true
  // Singularity configs, CHANGE THEM TO YOUR USED FILESYSTEM, if not properly set the container won't see your files
	runOptions = "-B /home -B /tmp"
	// where should the containers be downloaded to
	cacheDir = "${launchDir}/singularity_cache"
}

process {
  //Default executor for each process, other options can be e.g. SLURM.
  //See https://www.nextflow.io/docs/latest/executor.html for more options and details.
  executor='local'
}

//Default for total execution, remove this whole part if you are using a different option above than executor='local':
executor {
  cpus = 32
  memory = 200.GB
}