Hic dev

TOuCAN.nf

@@ -225,7 +225,7 @@ if(params.mode == "multiplot"){
 
 if (params.mode != "plot"){
 
-	if ( "${path_T2C_restriction_maps}" != ""){
+	if ( "${path_T2C_restriction_maps}" != "none"){
         if (! file ("${path_T2C_restriction_maps}/restriction_targets.bed").exists()){
             println("Warning: restriction_target.bed does not exists on given path (path_T2C_restriction_maps in configuration file) -> starting to create restriction maps.")
             create_res_map = true
@@ -371,7 +371,11 @@ process create_restriction_maps_for_T2C {
 	publishDir "${outpath}/${params.pn}_restriction_maps/", mode: 'copy'
 
 	output:
-	file ("*.bed") into restriction_maps
+	file ("restriction_sites_${params.enzyme_a_name}.bed") into restriction_maps_1
+    file ("restriction_fragments_${params.enzyme_a_name}.bed") into restriction_maps_2
+    file ("restriction_sites.bed") into restriction_maps_3
+    file ("restriction_fragments.bed") into restriction_maps_4
+    file ("restriction_targets.bed") into restriction_maps_5
 
 	when:
 	params.mode == 'T2C' || params.mode == 'multiplot'
@@ -407,10 +411,10 @@ process create_restriction_maps_for_T2C {
 	grep ${params.enzyme_a_sequence} restriction_fragments.bed > restriction_targets.bed
 	"""
 }
+restriction_maps = restriction_maps_1.concat(restriction_maps_2, restriction_maps_3, restriction_maps_4, restriction_maps_5)
 
 res_map.concat(restriction_maps).into {final_res_map_for_check; final_res_map; final_res_map_for_intersection; res_map_for_ifm}
 
-
 process check_restriction_maps {
 
 	tag{params.enzyme_a_name}
@@ -640,7 +644,6 @@ process samtools_sort {
 
 bam_f.concat(bamfiles).into {finalbam; bamfiles_for_flagstats; workaround}
 
-
 // T2C Step 6
 process samtools_flagstat {
 
@@ -692,7 +695,7 @@ process index_bamfiles {
 	"""
 }
 
-bam_bai_files_final = bam_bai_files.combine(workaround, by: 0)
+bam_bai_files.combine(workaround, by: 0).set {bam_bai_files_final}
 
 /*
 * T2C Step 8
@@ -1450,11 +1453,9 @@ process plot_TAD_graph {
 
 }
 
-multiplot_bed_1.concat(multiplot_bed_2).into {multiplot_bed_merged; testa}
+multiplot_bed_1.concat(multiplot_bed_2).set {multiplot_bed_merged}
+multiplot_TAD.join(multiplot_bed_merged).set {multi}
 
-multiplot_TAD.join(multiplot_bed_merged).into {multi; testb}
-testa.println()
-testb.println()
 
 process multiplot {
 

nextflow.config

@@ -5,12 +5,12 @@ env {
 	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_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 = "${path_working}/01_restriction_maps"		//If empty restriction maps are generated [typically: path_working + /01_restriction_maps/]. If empty files are generated
+	path_T2C_restriction_maps = "none"//"${path_working}/01_restriction_maps"		//If "none" restriction maps are generated [typically: path_working + /01_restriction_maps/]. If empty files are generated
 
 }
 
@@ -42,7 +42,7 @@ params {
 	//Parameter for HiC matrix
 	//--------------------------------------------
 	hicBuildMatrix_threads = 16
-	bwa_HiC_options = "-t 4" // bwa mem
+	bwa_HiC_options = "-t 16" // bwa mem
 	threads_bowtie2 = 12
 	inputBufferSize = 400000