nextflow.config

//Paths to dependencies
env {
	path_python = "/mnt/software/x86_64/packages/python/2.7.8-anaconda-5.1.0-stretch/bin"		//Path to python
	path_R = "/mnt/software/x86_64/packages/r/3.4.4-stretch-local/bin" //Path to R

	path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		// Path to parent folder containing bin folder with T2C analysis scripts.
	path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		// Working directory.

	path_genome = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe/index_bwa/GRCm38.p5.genome_whitelist.fa" 		// Path to full genome in fasta format + basis name of index [e.g. GRCm38.p5.genome_whitelist.fa]
	path_gtf = "/mnt/agnerds/Rene.Wiegandt/fromMario/gencode.vM15.annotation.gtf"

	path_T2C_restriction_maps = "none"//"${path_working}/01_restriction_maps"		//If "none" restriction maps are generated [typically: path_working + /01_restriction_maps/]. If empty files are generated

}

params {
	sample_extension = "_R[12]" // regex for sample extension [e.g "_R[12]_001" or "_R[12]"]

	// Enzyme Information
	// -------------------------------------------
	enzyme_a_name = "Hindiii"		// Name of first restriction enzyme. [e.g. Hindiii]
	enzyme_a_sequence = "AAGCTT"	// Sequence of first restriction enzyme [e.g. AAGCTT]
	enzyme_b_name = "NlaIII"		// Name of second restriction enzyme. [T2C only]
	enzyme_b_sequence = "GATG"		// Sequence of second restriction enzyme. [T2C only]

	// Minor fixed parameters for BWA and SAMtools
	// -------------------------------------------
	bwa_T2C_options = "-t 32" // bwa aln
	sort_options = "--threads 32"
	library_label = "capture"
	platform_label = "ILLUMINA"
	center_label = "ECB"

	//Parameter for normalization and plotting T2C
	// -------------------------------------------
	plot_options_T2C = ""
	norm_method = "array" //log, fpm, array and none

	uropa_threads = 32

	//Parameter for HiC matrix
	//--------------------------------------------
	hicBuildMatrix_threads = 16
	bwa_HiC_options = "-t 16" // bwa mem
	threads_bowtie2 = 12
	inputBufferSize = 400000

	//Parameter for uropa configuration
	uropa_feature = "" // "String,String,String,..."
	uropa_anchor = "" // "String,String,String,..."
	uropa_dist_1 = 1000
	uropa_dist_2 = 1000
	uropa_strand = "" // single argument "String"
	uropa_direction = "any_direction" // "String,String,String,..."
	uropa_filter_attr = "" // "String,String,String,..."
	uropa_attr_value = "" // "String,String,String,..."
	uropa_show_attr = "gene_id,gene_type,gene_name,level,transcript_type,transcript_support_level" // "String,String,String,..."

}

executor {
	name = "local"
	cpus = 48
	memory = '100 GB'
	//queueSize = 16 // cpus/threads in bwa aln
}