process {
withName:MarkDuplicates {
  memory = '50.GB'
}
withName:MapReads {
  memory = '100.GB'
}
withName:HaplotypeCaller {
  memory = '60.GB'
}
}

//Profile config names for nf-core/configs
params {
  config_profile_description = 'The Genotoul cluster profile'
  config_profile_contact = 'support.bioinfo.genotoul@inra.fr'
  config_profile_url = 'http://bioinfo.genotoul.fr/'
}
process.executor = "slurm"
singularity {
  // need one image per execution
  enabled = true
  runOptions = '-B /work/bank -B /bank -B /work2 -B /work -B /save -B /home -B /save/ng6'
}
params {
  genomes {
    'Gallus_gallus-5.0' {
        fasta     = "${params.genomes_base}/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa"
	fai       = "${params.genomes_base}/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.fai"
	//intervals = "${params.genomes_base}/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.bed"
	dict      = "${params.genomes_base}/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.dict"
	species   = 'Gallus_gallus'
	bwa       = "${params.genomes_base}/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.{amb,ann,bwt,pac,sa}"
	known_indels = "${params.genomes_base}/Gallus_gallus_incl_consequences.vcf"
	known_indels_index = "${params.genomes_base}/Gallus_gallus_incl_consequences.vcf.idx"
	}
    }
}

params {
  saveReference = true
  // Max resources requested by a normal node on genotoul.
  max_memory = 120.GB
  max_cpus = 10
  max_time = 96.h
}