nextflow.config

process {
	withLabel: 'process_high' { 
		cpus = 4
		memory = '16GB'
		time = '4h'
	}
	withLabel: 'process_medium' { 
		cpus = 2
		memory = '8GB'
		time = '1h'
	}
	withLabel: 'process_low' { 
		cpus = 1
		memory = '1GB'
		time = '1h'
	}

	withName: 'ariba_run' { 
		container = "https://depot.galaxyproject.org/singularity/ariba%3A2.14.6--py38h6ed170a_0" 
		memory = '32GB'
	}
	withName: 'ariba_summary' { 
		container = "https://depot.galaxyproject.org/singularity/ariba%3A2.14.6--py38h6ed170a_0" 
	}
	withName: 'bwa_*' { 
		container = "https://depot.galaxyproject.org/singularity/bwakit%3A0.7.15--3" 
		cpus = 16
		memory = '32GB'
		time = '1h'
	}
	withName: 'samtools_*' { 
		container = "https://depot.galaxyproject.org/singularity/ariba%3A2.14.6--py38h6ed170a_0" 
	}
	withName: 'spades' { 
		container = "https://depot.galaxyproject.org/singularity/spades%3A3.15.3--h95f258a_0" 
		cpus = 16
		memory = '64GB'
		time = '2h'
	}
	withName: quast { 
		container = "https://depot.galaxyproject.org/singularity/quast%3A5.0.2--py37pl526hb5aa323_2"
	}
	withName: mlst { 
		container = "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1" 
	}
	withName: kraken { 
		cpus = 16
		memory = '48GB'
		time = '2h'
		container = "https://depot.galaxyproject.org/singularity/kraken2%3A2.1.2--pl5262h7d875b9_0" 
	}
	withName: bracken { 
		cpus = 16
		memory = '48GB'
		time = '2h'
		container = "https://depot.galaxyproject.org/singularity/bracken%3A2.6.1--py39h7cff6ad_2" 
	}
	withName: freebayes { 
		container = "https://depot.galaxyproject.org/singularity/freebayes%3A1.3.5--py39hd2e4403_0" 
	}
	withName: 'chewbbaca_*' { 
		container = "https://depot.galaxyproject.org/singularity/chewbbaca%3A2.0.15--py36_0" 
		cpus = 7
	}
	withName: 'ariba_summary_to_json|post_align_qc' {
		container = "https://depot.galaxyproject.org/singularity/perl%3A5.26.2" 
    }
}

singularity {
	enabled = true
	runOptions = '--bind /fs1/:/fs1/ --bind /trannel/:/trannel/'
}

params {
	krakenDb = '/fs1/resources/ref/micro/krakenstd'
}

profiles {
	staphylococcus_aureus {
		params.genomeReference = '/fs1/resources/ref/micro/species/saureus/ref.fasta'
		params.aribaReference = '/fs1/resources/ref/micro/species/saureus/ariba/02.cdhit.all.fa'
		params.cgmlstDb = '/fs1/resources/ref/micro/species/saureus/cgmlst'
		params.trainingFile = '/fs1/resources/ref/micro/species/saureus/prodigal.trn'
	}

	escherichia_coli {
		params.genomeReference = '/fs1/resources/ref/micro/species/ecoli/ref.fasta'
		params.aribaReference = '/fs1/resources/ref/micro/species/ecoli/ariba/02.cdhit.all.fa'
		params.cgmlstDb = '/fs1/resources/ref/micro/species/ecoli/cgmlst'
		params.trainingFile = '/fs1/resources/ref/micro/species/ecoli/prodigal.trn'
	}

	klebsiella_pneumoniae {
		params.genomeReference = '/fs1/resources/ref/micro/species/klebsiella/ref.fasta'
		params.aribaReference = '/fs1/resources/ref/micro/species/klebsiella/ariba/02.cdhit.all.fa'
		params.cgmlstDb = '/fs1/resources/ref/micro/species/klebsiella/cgmlst'
		params.trainingFile = '/fs1/resources/ref/micro/species/klebsiella/prodigal.trn'
	}
}