diff --git a/RLIB/cis_matrix_body_multi.R b/RLIB/cis_matrix_body_multi.R
index 7c5cc02..da00fa3 100644
--- a/RLIB/cis_matrix_body_multi.R
+++ b/RLIB/cis_matrix_body_multi.R
@@ -47,7 +47,7 @@ require(plyr, quietly = TRUE)
 require(RColorBrewer, quietly = TRUE)
 require(gridExtra, quietly = TRUE)
 require(grid, quietly = TRUE)
-require(ggplot2 ,quietly = TRUE)
+##require(ggplot2 ,quietly = TRUE)
 require(ggpmisc, quietly = TRUE)
 if ( !(require("ggbio")) ) {
   biocLite("ggbio")
@@ -145,7 +145,7 @@ if(colour_range[2] == 0){
 #}
 
 wh <- GenomicRanges::GRanges(region[["chr"]], IRanges::IRanges(as.integer(region[["start"]]),as.integer(region[["end"]])))
-tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "tx_name")
+tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "gene_id")
 p2 <- tset@ggplot
 
 
@@ -154,7 +154,8 @@ palette <- c(
   rgb(0,0,255,maxColorValue=255),
   rgb(152,20,18,maxColorValue=255),
   rgb(240,48,0,maxColorValue=255),
-  rgb(255,188,39,maxColorValue=255))
+  rgb(255,188,39,maxColorValue=255),
+  rgb(124,252,0,maxColorValue=255))
 
 # triangle plot
 message(paste("Constructing plot"))
@@ -162,7 +163,7 @@ p <- ggplot2::ggplot()
 p <- p + geom_polygon(aes(x=x, y=y, group=group), fill="black", data=rotated_bg)
 if(add_borders_to_elements){
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal, colour=signal), data=rotated_data, size=0.2)
-  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green")
+  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green", guide = "colourbar")
 } else {
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal), data=rotated_data)
 }
diff --git a/TOuCAN.nf b/TOuCAN.nf
index 812f73a..4b294f7 100644
--- a/TOuCAN.nf
+++ b/TOuCAN.nf
@@ -23,6 +23,10 @@ params.int_score = 50
 
 params.aln = "bwa"
 params.bin = 100000
+params.hic_thresh_min = -1.5
+params.hic_thresh_max = 5
+params.inputBufferSize = 400000
+params.bt2_index_threads = 4
 
 if(params.mode == "help" || params.mode == "h"){
 log.info """
@@ -77,7 +81,8 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi
 		--end [INT]			- End of target region.
 		--score_min [INT]		- Score range: minimum. [default: 0]
 		--score_max [INT]		- Score range: maximium. [default: autoscale]
-                --pn [STRING]                  - Name of the Project [default: 'Project']
+                --pn [STRING]                  - Name of the project [default: 'Project']
+                --organsim [mm10,mm9,hg19]     - Type of the genome
 
 --mode uropa			   	       - Uropa annoation [T2C]
 	parameters:
@@ -88,7 +93,7 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi
 		--end [INT]			- End of target region.
                 --pn [STRING]                  - Name of the Project [default: 'Project']
 
---mode multiplot			       - creating a plot with interaction map, TAD graph and gene annotation
+--mode multiplot			       - Creating a plot with interaction map, TAD graph and gene annotation
 	parameters:
 		--in [PATH]			- Path to directory with *.normalized.bed
 		--out [PATH]			- Path to output directory.
@@ -105,6 +110,10 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi
 		--out [PATH]			- Path to output directory.
 		--aln [bwa|bowtie2]		- Choose alignment tool. [default: bwa]
 		--bin [INT]			- Binsize [default: 10000]
+        --hic_thresh_min [(-)INT]   - Threshold filter miniumum [default: -1.5]
+        --hic_thresh_max [INT]      - Threshold filter maximum [default: 5]
+        --inputBufferSize [INT]     - Buffersize for creating hic matrix [default: 400000]
+        --bt2_index_threads [INT]   - Number of threads used or creating bt2 index
 
 Skip Aligment -> BAM files as Input:
 The BAM files need to be from this Pipeline with follwing
@@ -156,12 +165,6 @@ Chromosome: ${params.chr}
 Start: ${params.start}
 End: ${params.end}
 
-Dependencies
-Python: ${path_python}
-BWA: ${path_bwa}
-samtools: ${path_samtools}
-bedtools: ${path_bedtools}
-
 Path to bin: ${path_bin}
 Path to genome: ${path_genome}
 Path to restriction maps: ${path_T2C_restriction_maps}
@@ -219,9 +222,14 @@ if(params.mode == "multiplot"){
 
 if (params.mode != "plot"){
 
-	if ( "${path_T2C_restriction_maps}" != "" ){
+	if ( "${path_T2C_restriction_maps}" != ""){
+        if (! file ("${path_T2C_restriction_maps}/restriction_targets.bed").exists()){
+            println("Warning: restriction_target.bed does not exists on given path (path_T2C_restriction_maps in configuration file) -> starting to create restriction maps.")
+            create_res_map = true
+        } else {
 		res_map = Channel.fromPath("${path_T2C_restriction_maps}/*.bed")
 		create_res_map = false
+        }
 	} else {
 		create_res_map = true
 	}
@@ -384,7 +392,7 @@ process check_output_directory {
 */
 process create_restriction_maps_for_T2C {
 
-	publishDir "${outpath}/${params.pn}_restriction_maps/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_restriction_maps/", mode: 'copy'
 
 	output:
 	file ("*.bed") into restriction_maps
@@ -451,7 +459,7 @@ process decompress {
 	tag{fastqGz}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_fastq/", mode: 'move', overwrite: 'false'
+		publishDir "${outpath}/${params.pn}_fastq/", mode: 'copy', overwrite: 'false'
 	}
 
 	input:
@@ -481,6 +489,8 @@ process decompress {
 
 process create_bwa_index {
 
+    conda "$workflow.projectDir/envtoucan.yaml"
+
 	output:
 	file ('f') into index
 	file ('f') into index_hic_bwa
@@ -503,7 +513,7 @@ process create_bwa_index {
 		"""
 	else
 		"""
-		${path_bwa}/bwa index ${path_genome}
+		bwa index ${path_genome}
 		echo done > f
 		"""
 
@@ -513,12 +523,15 @@ process create_bwa_index {
 // T2C Step 2
 process bwa_aln {
 
+    //conda 'bioconda::bwa=0.7.15'
+    conda "$workflow.projectDir/envtoucan.yaml"
+
 	tag{fastq}
 
 	executor 'local'
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/sai/", mode: 'move', pattern: '*.sai'
+		publishDir "${outpath}/${params.pn}_additional_files/sai/", mode: 'copy', pattern: '*.sai'
 	}
 
 	input:
@@ -533,7 +546,7 @@ process bwa_aln {
 
 	script:
 	"""
-	${path_bwa}/bwa aln \
+	bwa aln \
 		${params.bwa_T2C_options} \
 		${path_genome} \
 		$fastq > ${fastqName}.sai
@@ -544,9 +557,9 @@ process bwa_aln {
 process bwa_sampe_to_create_sam {
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/sam/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/sam/", mode: 'copy'
 	}
-
+    conda "$workflow.projectDir/envtoucan.yaml"
 	tag{name}
 
 	input:
@@ -560,8 +573,8 @@ process bwa_sampe_to_create_sam {
 	create_bam == true
 
 	script:
-	fullname = sai[0].simpleName
-	if(fullname.contains("_R1")){
+    sortbasename = [sai[0].getBaseName(), sai[1].getBaseName()].sort()
+	if(sai[0].contains(sortbasename[0])){
 		sai_R1 = sai[0]
 		fastq_R1 = fastq[0]
 		sai_R2 = sai[1]
@@ -574,7 +587,7 @@ process bwa_sampe_to_create_sam {
 	}
 
  	"""
-	${path_bwa}/bwa sampe \
+	bwa sampe \
 		-A \
 		${path_genome} \
 		${sai_R1} ${sai_R2} \
@@ -587,9 +600,10 @@ process bwa_sampe_to_create_sam {
 process samtools_addreplacerg {
 
 	tag{sam}
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/sam/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/sam/", mode: 'copy'
 	}
 
 	input:
@@ -605,7 +619,7 @@ process samtools_addreplacerg {
 	script:
 	ds = "${path_working}/*.srt.bam"
 	"""
-	${path_samtools}/samtools addreplacerg \
+	samtools addreplacerg \
 				-r "ID:${name}" \
 				-r "CN:${params.center_label}" \
 				-r "LB:${params.library_label}" \
@@ -622,8 +636,9 @@ process samtools_addreplacerg {
 process samtools_sort {
 
 	executor 'local'
+    conda "$workflow.projectDir/envtoucan.yaml"
 
-	publishDir "${outpath}/${params.pn}_bam/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_bam/", mode: 'copy'
 
 	tag{rgsam}
 
@@ -639,7 +654,7 @@ process samtools_sort {
 
 	script:
 	"""
-	${path_samtools}/samtools sort \
+	samtools sort \
 					   ${params.sort_options} \
 					   -T ${name}_tmp_sort \
 					   -o ${name}.bam \
@@ -647,15 +662,15 @@ process samtools_sort {
 	"""
 }
 
-bam_f.concat(bamfiles).into {finalbam; bamfiles_for_flagstats;}
+bam_f.concat(bamfiles).into {finalbam; bamfiles_for_flagstats; workaround}
 
 
 // T2C Step 6
 process samtools_flagstat {
 
-	publishDir "${outpath}/${params.pn}_stats/", mode: 'move'
-
-	tag{bam}
+	publishDir "${outpath}/${params.pn}_stats/", mode: 'copy'
+    conda "$workflow.projectDir/envtoucan.yaml"
+    tag{bam}
 
 	input:
 	set name, file (bam) from bamfiles_for_flagstats
@@ -668,7 +683,7 @@ process samtools_flagstat {
 
 	script:
 	"""
-	${path_samtools}/samtools flagstat ${bam} > ${name}.flagstat.txt
+	samtools flagstat ${bam} > ${name}.flagstat.txt
 	"""
 }
 
@@ -680,26 +695,28 @@ process samtools_flagstat {
 process index_bamfiles {
 
 	tag{bam}
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bai/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bai/", mode: 'copy'
 	}
 
 	input:
 	set name, file (bam) from finalbam
 
 	output:
-	set name, file ("${name}.bam.bai"), file ("${bam}") into bam_bai_files
+	set name, file ("${name}.bam.bai") into bam_bai_files, test
 
 	when:
 	params.mode == "T2C"
 
 	script:
 	"""
-	${path_samtools}/samtools index ${bam} > ${name}.bam.bai
+	samtools index ${bam} > ${name}.bam.bai
 	"""
 }
 
+bam_bai_files_final = bam_bai_files.combine(workaround, by: 0)
 
 /*
 * T2C Step 8
@@ -712,11 +729,11 @@ process overlapping_reads_targets {
 	executor 'local'
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'copy'
 	}
 
 	input:
-	set name, file (bai), file (bam), file (res_target) from bam_bai_files.combine(final_res_map.filter{ it.simpleName == "restriction_targets"})
+	set name, file (bai), file (bam), file (res_target) from bam_bai_files_final.combine(final_res_map.filter{ it.simpleName == "restriction_targets"})
 
 	output:
 	set name, file ("${name}.target.bam") into target_bam_files
@@ -741,9 +758,10 @@ process overlapping_reads_targets {
 process namesorting_bam_files {
 
 	tag{target_bam}
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'copy'
 	}
 
 	input:
@@ -757,7 +775,7 @@ process namesorting_bam_files {
 
 	script:
 	"""
-	${path_samtools}/samtools sort \
+	samtools sort \
 		-n \
 		-o ${name}.namesort.bam \
 		${target_bam}
@@ -777,9 +795,10 @@ process namesorting_bam_files {
 process filter_aligments {
 
 	tag{namesort_bam}
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bam/", mode: 'copy'
 	}
 
 	input:
@@ -793,7 +812,7 @@ process filter_aligments {
 
 	script:
 	"""
-	${path_samtools}/samtools view -h \
+	samtools view -h \
  		-f 0x0001 \
 		-F 0x0004 \
 		-F 0x0008 \
@@ -813,7 +832,7 @@ process create_matrix {
 	tag{filtered_bam}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
 	}
 
 	input:
@@ -842,7 +861,7 @@ process finish_raw_matrix {
 	tag{reads_bed}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
 	}
 
 	input:
@@ -874,7 +893,7 @@ process	split_matrix_for_re_evaluation {
 	tag{matrix_bed}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
 	}
 
 	input:
@@ -903,7 +922,7 @@ process intersect_beds_to_fragments {
 	tag{name}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
 	}
 
 	input:
@@ -931,7 +950,7 @@ process reassign_matrix {
 	tag{matrix}
 
 	if(params.safe_all_files == 1){
-		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
 	}
 
 	input:
@@ -960,7 +979,7 @@ process finalize_matrix {
 
 	tag{temp_bed}
 
-	publishDir "${outpath}/${params.pn}_Interactions/01_all_interactions_bed_raw/", mode: 'move', pattern: "${name_raw}.reassigned.bed"
+	publishDir "${outpath}/${params.pn}_Interactions/01_all_interactions_bed_raw/", mode: 'copy', pattern: "${name_raw}.reassigned.bed"
 
 	input:
 	set name, file (temp_bed) from temp_bed_file
@@ -989,7 +1008,7 @@ process normalize_matrix {
 
 	tag{matrix}
 
-	publishDir "${outpath}/${params.pn}_Interactions/02_all_interactions_bed_norm/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_Interactions/02_all_interactions_bed_norm/", mode: 'copy'
 
 	input:
 	set name, file (matrix) from reassigned_matrix
@@ -1002,7 +1021,7 @@ process normalize_matrix {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/normalize_paired_bed.R --bedfile ${matrix} \
+	${path_R}/Rscript ${path_bin}/bin/normalize_paired_bed.R --bedfile ${matrix} \
     	--outfile ${name}.normalized.bed \
     	--library ${path_bin}/RLIB/ \
     	--method ${params.norm_method}
@@ -1020,9 +1039,9 @@ process plotting {
 	tag{name}
 
 	if(params.mode == "plot" ){
-		publishDir "${outpath}/plot/", mode: 'move'
+		publishDir "${outpath}/plot/", mode: 'copy'
 	} else {
-		publishDir "${outpath}/${params.pn}_plots/interaction_plot/", mode: 'move'
+		publishDir "${outpath}/${params.pn}_plots/interaction_plot/", mode: 'copy'
 	}
 
 	input:
@@ -1036,7 +1055,7 @@ process plotting {
 
 	script:
 	"""
-	Rscript  ${path_bin}/bin/plot_cis_matrix.R \
+	${path_R}/Rscript  ${path_bin}/bin/plot_cis_matrix.R \
 	    --bedfile ${matrix} \
 	    --outfile ${name}.cis.pdf \
 	    --library ${path_bin}/RLIB/ \
@@ -1056,7 +1075,7 @@ process create_interaction_table {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_Interactions/03_target_region_interactions_bed/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_Interactions/03_target_region_interactions_bed/", mode: 'copy'
 
 	input:
 	set name, file (norm) from filtered_interaction_bed_final_merge
@@ -1069,7 +1088,7 @@ process create_interaction_table {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/create_interaction_table.R \
+	${path_R}/Rscript ${path_bin}/bin/create_interaction_table.R \
 		${norm} ${name}.filtered.interactions.bed \
 		${params.chr} ${params.start} ${params.end} ${params.int_score} \
 		$workflow.workDir/${name}.filtered.interactions.bed
@@ -1081,7 +1100,7 @@ process create_stats {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_stats/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_stats/", mode: 'copy'
 
 	input:
 	set name, file (reads) from reads_bed_files_for_stats
@@ -1094,7 +1113,7 @@ process create_stats {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/create_T2C_stats.R \
+	${path_R}/Rscript ${path_bin}/bin/create_T2C_stats.R \
 		${reads} ${name}_stats.pdf \
 		${params.chr} ${params.start} ${params.end} ${name}
 	"""
@@ -1117,8 +1136,8 @@ process create_uropa_config_1 {
 
 
 	script:
-    config_parameters = [uropa_feature,uropa_anchor,uropa_strand,uropa_direction,
-                        uropa_filter_attr,uropa_attr_value,uropa_show_attr]
+    config_parameters = [params.uropa_feature,params.uropa_anchor,params.uropa_strand,params.uropa_direction,
+                        params.uropa_filter_attr,params.uropa_attr_value,params.uropa_show_attr]
 
     conf_list = config_parameters.collect { par ->
         return "\\\"" + par.replace(",","\\\",\\\"") + "\\\""
@@ -1159,9 +1178,10 @@ process create_uropa_config_1 {
 process run_uropa_1 {
 
 	tag{name}
+    conda "$workflow.projectDir/uropa.yaml"
 
     if(params.safe_all_files == 1){
-	       publishDir "${outpath}/${params.pn}_uropa/", mode: 'move'
+	       publishDir "${outpath}/${params.pn}_uropa/", mode: 'copy'
     }
 
 	input:
@@ -1194,7 +1214,7 @@ process swap_fragments {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/swap_fragments.R ${int_bed} ${name}.swap.interaction.bed $workflow.workDir/${name}.swap.interaction.bed
+	${path_R}/Rscript ${path_bin}/bin/swap_fragments.R ${int_bed} ${name}.swap.interaction.bed $workflow.workDir/${name}.swap.interaction.bed
 	"""
 }
 
@@ -1214,8 +1234,8 @@ process create_uropa_config_2 {
 
 	script:
 
-    config_parameters = [uropa_feature,uropa_anchor,uropa_strand,uropa_direction,
-                        uropa_filter_attr,uropa_attr_value,uropa_show_attr]
+    config_parameters = [params.uropa_feature,params.uropa_anchor,params.uropa_strand,params.uropa_direction,
+                        params.uropa_filter_attr,params.uropa_attr_value,params.uropa_show_attr]
 
     conf_list = config_parameters.collect { par ->
         return "\\\"" + par.replace(",","\\\",\\\"") + "\\\""
@@ -1257,9 +1277,10 @@ process create_uropa_config_2 {
 process run_uropa_2 {
 
 	tag{name}
+    conda "$workflow.projectDir/uropa.yaml"
 
     if(params.safe_all_files == 1){
-           publishDir "${outpath}/${params.pn}_uropa/", mode: 'move'
+           publishDir "${outpath}/${params.pn}_uropa/", mode: 'copy'
     }
 
 	input:
@@ -1284,7 +1305,7 @@ process uropa_merge {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_Interactions/04_final_interactions_annotated/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_Interactions/04_final_interactions_annotated/", mode: 'copy'
 
 	input:
 	set name, file (allhits_1), file (finalhits_1), file (allhits_2), file (finalhits_2), file (int_bed) from final_uropa_set
@@ -1298,7 +1319,7 @@ process uropa_merge {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/merge_uropa_interactions.R ${int_bed} ${finalhits_1} ${finalhits_2} ${name}.finalhits.merged.txt
+	${path_R}/Rscript ${path_bin}/bin/merge_uropa_interactions.R ${int_bed} ${finalhits_1} ${finalhits_2} ${name}.finalhits.merged.txt
 	"""
 
 }
@@ -1308,7 +1329,7 @@ xlsx_list = for_xlsx.toSortedList()
 process xlsx_writer {
 
 
-    publishDir "${outpath}/", mode: 'move'
+    publishDir "${outpath}/", mode: 'copy'
 
     input:
     val f from xlsx_list
@@ -1335,7 +1356,7 @@ process create_viewpoint {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_Interactions/05_interactions_viewpoint_annotated/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_Interactions/05_interactions_viewpoint_annotated/", mode: 'copy'
 
 	input:
 	set name, file (merged_finalhits) from merged_uropa
@@ -1348,7 +1369,7 @@ process create_viewpoint {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/create_interaction_viewpoint.R ${merged_finalhits} ${name}.interactions.viewpoint.txt
+	${path_R}/Rscript ${path_bin}/bin/create_interaction_viewpoint.R ${merged_finalhits} ${name}.interactions.viewpoint.txt
 	"""
 }
 
@@ -1359,7 +1380,7 @@ process convert_to_IFMatrix {
 	tag{name}
 
     if(params.safe_all_files == 1){
-	       publishDir "${outpath}/${params.pn}_additional_files/IFMatrix/", mode: 'move'
+	       publishDir "${outpath}/${params.pn}_additional_files/IFMatrix/", mode: 'copy'
     }
 
 	input:
@@ -1373,7 +1394,7 @@ process convert_to_IFMatrix {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/convert_to_IFMatrix.R ${int_bed} ${name}.ifm.txt
+	${path_R}/Rscript ${path_bin}/bin/convert_to_IFMatrix.R ${int_bed} ${name}.ifm.txt
 	"""
 }
 
@@ -1382,32 +1403,52 @@ process run_robusTAD {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_TAD/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_TAD/", mode: 'copy'
 
 	input:
 	set name, file (tfm) from ifmatrix
 
 	output:
-	set name, file ("TADBoundaryCalls_*.txt") into tadbc, multiplot_TAD
+	set name, file ("TADBoundaryCalls_*.txt") into tadbc
 
 	when:
 	params.mode == "T2C" || params.mode == "multiplot"
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/RobusTAD.R -i ${tfm} --header FALSE -n norm
+	${path_R}/Rscript ${path_bin}/bin/RobusTAD.R -i ${tfm} --header FALSE -n norm
 	"""
 }
 
+process x_axis_scaling {
+
+  tag{name}
+
+  input:
+  set name, file (tad) from tadbc
+
+  output:
+  set name, file ("${bn}.txt") into tadx, multiplot_TAD
+
+  when:
+  params.mode == "T2C" || params.mode == "multiplot"
+
+  script:
+  bn = tad.baseName
+  """
+  ${path_R}/Rscript ${path_bin}/bin/xaxis_scaling.R ${tad} ${params.start} ${params.end} ${bn}.txt
+  """
+}
+
 
 process plot_TAD_graph {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_plots/TAD/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_plots/TAD/", mode: 'copy'
 
 	input:
-	set name, file (tad) from tadbc
+	set name, file (tad) from tadx
 
 	output:
 	file ("${name}.TAD.pdf")
@@ -1417,7 +1458,7 @@ process plot_TAD_graph {
 
 	script:
 	"""
-	Rscript ${path_bin}/bin/plotTAD.R ${tad} ${name}.TAD.pdf
+	${path_R}/Rscript ${path_bin}/bin/plotTAD.R ${tad} ${name}.TAD.pdf
 	"""
 
 }
@@ -1428,7 +1469,7 @@ process multiplot {
 
 	tag{name}
 
-	publishDir "${outpath}/${params.pn}_plots/multiplot/", mode: 'move'
+	publishDir "${outpath}/${params.pn}_plots/multiplot/", mode: 'copy'
 
 	input:
 	set name, file (tad) from multiplot_TAD
@@ -1442,7 +1483,7 @@ process multiplot {
 
 	script:
 	"""
-	Rscript  ${path_bin}/bin/plot_multi.R \
+	${path_R}/Rscript  ${path_bin}/bin/plot_multi.R \
 	    --bedfile ${bed} \
 	    --outfile ${name}.multi.png \
 	    --library ${path_bin}/RLIB/ \
@@ -1462,7 +1503,7 @@ for_pptx_list = for_pptx.toSortedList()
 process pptx_writer {
 
 
-    publishDir "${outpath}/", mode: 'move'
+    publishDir "${outpath}/", mode: 'copy'
 
     input:
     val pptxList from for_pptx_list
@@ -1516,6 +1557,8 @@ if(params.aln == "bwa"){
 process alignment_with_bwa {
 
 	tag{fastq}
+    publishDir "${outpath}/bam/", mode: 'copy'
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	input:
 	set basisname, fastqName ,file (fastq) from decompressedfastq_for_HiC_bwa
@@ -1529,7 +1572,7 @@ process alignment_with_bwa {
 
 	script:
 	"""
-	${path_bwa}/bwa mem \
+	bwa mem \
 		${params.bwa_HiC_options} \
 		${path_genome} \
 		$fastq | ${path_samtools}/samtools view -Shb > ${fastqName}.bam
@@ -1539,14 +1582,20 @@ process alignment_with_bwa {
 
 process bowtie2_index {
 
+    publishDir "${path_genome}", mode: 'copy'
+    conda "$workflow.projectDir/envtoucan.yaml"
+
 	when:
 	params.mode == "HiC" && params.aln == "bowtie2"
 
+    output:
+    val ("${genome_name}") into index_bt2
+
 	script:
 	genome_file = file (path_genome)
 	genome_name = genome_file.name
 	"""
-	${path_bowtie2}/bowtie2-build ${path_genome} ${genome_name}
+	bowtie2-build ${path_genome} ${genome_name} --threads ${params.bt2_index_threads}
 	"""
 }
 
@@ -1554,9 +1603,12 @@ process bowtie2_index {
 process alignment_with_bowtie2 {
 
 	tag{fastq}
+    publishDir "${outpath}/bam/", mode: 'copy'
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	input:
 	set basisname, fastqName ,file (fastq) from decompressedfastq_for_HiC_bowtie2
+    val bt2_idx from index_bt2
 
 	output:
 	set basisname, file ("${fastqName}.bam") into bowtie2_alignment
@@ -1566,8 +1618,8 @@ process alignment_with_bowtie2 {
 
 	script:
 	"""
-	${path_bowtie2}/bowtie2 -x ${path_genome} -U ${fastq} --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder -p 12 \
-	| ${path_samtools}/samtools view -Shb - > ${fastqName}.bam
+	bowtie2 -x ${path_genome} -U ${fastq} --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder -p 12 \
+	| samtools view -Shb - > ${fastqName}.bam
 	"""
 }
 
@@ -1576,6 +1628,7 @@ hic_alignment = bwa_alignment.concat(bowtie2_alignment) //.concat(histat_alignme
 process create_HiC_matrix {
 
 	tag{name}
+    publishDir "${outpath}/h5_matrix/", mode: 'copy'
 
 	input:
 	set name, bams from hic_alignment.groupTuple()
@@ -1588,13 +1641,20 @@ process create_HiC_matrix {
 	params.mode == "HiC"
 
 	script:
-	bam_r1 = bams[0]
-	bam_r2 = bams[1]
+    sortbasename = [bams[0].getBaseName(), bams[1].getBaseName()].sort()
+    if(bams[0].contains(sortbasename[0])){
+        bam_r1 = bams[0]
+	    bam_r2 = bams[1]
+    } else {
+        bam_r1 = bams[1]
+	    bam_r2 = bams[0]
+    }
 	"""
 	hicBuildMatrix --samFiles ${bam_r1} ${bam_r2} \
 				 --QCfolder ${outpath}/QC_${name}/  \
                  --binSize ${params.bin} \
 				 -b ${name}.bam \
+                 --inputBufferSize ${params.inputBufferSize} \
                  --restrictionSequence ${params.enzyme_a_sequence} \
                  -o ${name}_matrix.h5
 
@@ -1604,7 +1664,7 @@ process create_HiC_matrix {
 
 process diagnostic_plot_of_HiC_Matrix {
 
-    publishDir "${outpath}/diagnostic_plots/", mode: 'move'
+    publishDir "${outpath}/diagnostic_plots/", mode: 'copy'
 
 	input:
 	set name, file (matrix) from hic_matrix_for_diagnostic
@@ -1633,14 +1693,14 @@ process correct_matrix {
 
     script:
     """
-    hicCorrectMatrix correct -m ${matrix} --filterThreshold -1.5 5 -o ${name}_corrected.h5
+    hicCorrectMatrix correct -m ${matrix} --filterThreshold ${params.hic_thresh_min} ${params.hic_thresh_max} -o ${name}_corrected.h5
     """
 }
 
 
 process plot_matrix {
 
-    publishDir "${params.out}/plot/", mode: 'move'
+    publishDir "${outpath}/plot/", mode: 'copy'
 
 	input:
 	set name, file (corrected_matrix) from hic_matrix_corrected
@@ -1654,6 +1714,6 @@ process plot_matrix {
 	script:
 	"""
 	hicPlotMatrix -m ${corrected_matrix} -o ${name}.hic.matrix.png \
-            --chromosomeOrder chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY
+    --dpi 400 --region ${params.chr}:${params.start}-${params.end}
 	"""
 }
diff --git a/bin/xaxis_scaling.R b/bin/xaxis_scaling.R
new file mode 100644
index 0000000..48d517e
--- /dev/null
+++ b/bin/xaxis_scaling.R
@@ -0,0 +1,19 @@
+#!/usr/bin/env Rscript
+args <- commandArgs(trailingOnly=TRUE)
+
+path <- args[1]
+start <- as.numeric(args[2])
+end <- as.numeric(args[3])
+out <- args[4] #"./out.txt"
+
+tad <- data.table::fread(path, header = TRUE , sep = ' ')
+xaxis <- tad[,1]
+xmax <- max(xaxis)
+
+newxaxis <- lapply(xaxis, function(x){
+  new_x <- (((end - start) * x) / xmax) + start
+})
+
+tad[,1] <- round(unlist(newxaxis[1]))
+
+data.table::fwrite(tad, file = out, col.names = TRUE, sep = ' ', quote = FALSE)
diff --git a/envtoucan.yaml b/envtoucan.yaml
new file mode 100644
index 0000000..ee602a2
--- /dev/null
+++ b/envtoucan.yaml
@@ -0,0 +1,10 @@
+name: envtoucan
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - bwa=0.7.15
+  - samtools=1.3.1
+  - bedtools=2.27.1
+  - bowtie2=2.3.3.1
diff --git a/multiplot.png b/multiplot.png
index 5a06049..f5fa0db 100755
Binary files a/multiplot.png and b/multiplot.png differ
diff --git a/nextflow.config b/nextflow.config
index 4f7902d..03f9dd4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,35 +1,21 @@
 
 //Paths to dependencies
 env {
-	path_bowtie2 = "/mnt/software/x86_64/packages/bowtie2/2.3.3.1/" //Path to bowtie2
 	path_python = "/mnt/software/x86_64/packages/python/2.7.8-anaconda-5.1.0-stretch/bin"		//Path to python
-	path_bwa = "/mnt/software/x86_64/packages/bwa/0.7.12/bin"		//Path to bwa
-	path_samtools = "/mnt/software/x86_64/packages/samtools/1.3.1/bin"	//Path to samtools
-	path_bedtools = "/mnt/software/x86_64/packages/bedtools/2.27.1/bin"	//Path to bedtools
+	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/THCPipe"		// Path to T2C analysis scripts
-	path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe"		//Path to directory where files are stored. If restriction maps are already existing put them in folder 01_restriction_maps inside this working_dir
+	path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		// Path to T2C analysis scripts
+	path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		//Path to directory where files are stored. If restriction maps are already existing put them in folder 01_restriction_maps inside this working_dir
 
 	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_bam_files = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe/temp/"  //Path to alingment files. If empty files are generated
-
-	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,..."
 
 }
 
 params {
-	sample_extension = "_R[12]_001"//"_R[12]_001" // regex for sample extension [e.g "_R[12]_001" or "_R[12]"]
+	sample_extension = "_R[12]_001" // regex for sample extension [e.g "_R[12]_001" or "_R[12]"]
 
 	// Enzyme Information
 	// -------------------------------------------
@@ -40,8 +26,8 @@ params {
 
 	// Minor fixed parameters for BWA and SAMtools
 	// -------------------------------------------
-	bwa_T2C_options = "-t 4" // bwa aln
-	sort_options = "--threads 4"
+	bwa_T2C_options = "-t 16" // bwa aln
+	sort_options = "--threads 16"
 	library_label = "capture"
 	platform_label = "ILLUMINA"
 	center_label = "ECB"
@@ -55,9 +41,19 @@ params {
 
 	//Parameter for HiC matrix
 	//--------------------------------------------
-	hicBuildMatrix_options = "--threads 4 --inputBufferSize 100000"
-	bwa_HiC_options = "" // bwa mem
+	hicBuildMatrix_options = "--threads 16 --inputBufferSize 100000"
+	bwa_HiC_options = "-t 4" // bwa mem
 
+	//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,..."
 
 }
 
diff --git a/uropa.yaml b/uropa.yaml
new file mode 100755
index 0000000..ee0e212
--- /dev/null
+++ b/uropa.yaml
@@ -0,0 +1,8 @@
+name: uropa
+
+channels:
+  - bioconda
+  - conda-forge
+
+dependencies:
+  - uropa