nextflow.config

params {
	readDir = "reads"
	resultsDir = "results"
	library = "library.txt"
	barcodes = 'barcodes.txt'
	forward_stranded = true
	barcode_random_length = 6
	barcode_demux_mismatches = 1
	barcode_demux_length = 4
	spacer_length = 20
	padding_base = 'G'
}

timeline {
	enabled = true
}

singularity {
	enabled = true
}

process {
	container = 'docker://zuberlab/crispr-nf'
	errorStrategy = 'retry'
	maxRetries = 3
	maxForks = 20

	cpus = 1
	time = { 1.h * task.attempt }
	memory = { 1.GB * task.attempt }

	$bam_to_fastq {
		cpus = 2
		time = { 2.h * task.attempt }
	}
	$trim_random_barcode {
		cpus = 2
		time = { 2.h * task.attempt }
	}
	$demultiplex {
		cpus = 2
		time = { 2.h * task.attempt }
	}
	$trim_barcode_and_spacer {
		cpus = 2
		time = { 2.h * task.attempt }
	}
	$align {
		cpus = { 6 * task.attempt }
		memory = { 3.GB * task.attempt }
	}
	$fastqc {
		time = { 2.h * task.attempt }
		memory = 10.GB
	}
	$count {
		cpus = 2
		memory = { 3.GB * task.attempt}
	}
	$combine_counts {
		memory = { 3.GB * task.attempt}
	}
}

profiles {

    standard {
        process.executor = 'local'
		process.container = '/groups/zuber/zubarchive/GROUPS/Bioinfo/singularity/crispr-nf.img'
		process.maxForks = 3
    }

    sge {
		process.executor = 'sge'
		process.penv = 'smp'
		process.queue = 'public.q'
		process.container = '/groups/zuber/zubarchive/GROUPS/Bioinfo/singularity/crispr-nf.img'
    }

	slurm {
		process.executor = 'slurm'
		process.clusterOptions = '--qos=short'
	}

	local {
		process.executor = 'local'
		singularity.enabled = false
		process.maxForks = 3
	}
}