diff --git a/README.md b/README.md
index 3df7827..ce23475 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ T2C Analysis:
   * raw/normalized
 * bed file with all interactions inside the target region
   * with and without uropa annotation
-* easy to read viewpoint format for annotated interactions (see Results for explanation) 
+* easy to read viewpoint format for annotated interactions (see Results for explanation)
 * restriction maps for different runs on the genome
 
 HiC Analysis:
@@ -31,7 +31,7 @@ Note: Green shows a value higher than the scale.
 ## Installation and Command-line usage
 ### Dependencies
 * Linux
-* Nextflow version 0.27.6.4775
+* Nextflow version 0.30
 * R version version 3.4.4
   * ggplot2
   * plyr
@@ -45,12 +45,15 @@ Note: Green shows a value higher than the scale.
 * Python version 2.7.8
   * pysam
   * getopt
-* bowtie2 version 2.3.3.1
-* bwa version 0.7
-* SAMtools version 1.3.1
-* BEDtools version 2.27
-* uropa version 2.0.2 alpha
 * HiCExplorer version 2.1
+* Conda:
+  * bowtie2 version 2.3.3.1*
+  * bwa version 0.7*
+  * SAMtools version 1.3.1*
+  * BEDtools version 2.27*
+  * uropa version 2.0.2 alpha*  
+  
+``* Will be implemented automatically through conda enviroment.``
 
 ### Installation
 To install Nextflow, follow the instructions on the offical Nextflow [website](https://www.nextflow.io/).
@@ -148,7 +151,3 @@ nextflow run TOuCAN.nf --mode T2C --in /example/fastq/ --out /out/ --chr chr1 --
 
 ## Results
 For a detailed explanation of all Results, follow this [link](https://github.molgen.mpg.de/loosolab/TOuCAN/wiki/TOuCAN-Results).
-
-
-
-
diff --git a/TOuCAN.nf b/TOuCAN.nf
index 4b294f7..a2a346b 100644
--- a/TOuCAN.nf
+++ b/TOuCAN.nf
@@ -9,6 +9,7 @@ params.safe_all_files = 0
 params.check_res_maps = 0
 params.organism = "mm10"
 params.pn = "Project"
+params.reassin = 0
 
 // parameter for T2C plots
 params.chr = ""
@@ -103,10 +104,12 @@ Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi
                 --score_min [INT]		- Score range: minimum. [default: 0]
                 --score_max [INT]		- Score range: maximium. [default: autoscale]
                 --pn [STRING]                  - Name of the Project [default: 'Project']
+                --organsim [mm10,mm9,hg19]     - Type of the genome
 
 --mode HiC 					- Full HiC analysis
 	parameters:
 		--in [PATH]			- Path to directory with fastq / fastq.gz files.
+        --bam [PATH]                   - Path to directory with bam files. Two bam files (forward + reversed) are required per sample. [if given --in [PATH] is ignored]
 		--out [PATH]			- Path to output directory.
 		--aln [bwa|bowtie2]		- Choose alignment tool. [default: bwa]
 		--bin [INT]			- Binsize [default: 10000]
@@ -194,8 +197,10 @@ multiplot_bed_1 = Channel.empty()
 matrix_to_plot = Channel.empty()
 res_map = Channel.empty()
 bam_f = Channel.empty()
+bam_f2 = Channel.empty()
 interaction_uropa = Channel.empty()
 fastqGzFiles = Channel.empty()
+hic_matrix_f = Channel.empty()
 
 if("${params.path_matrix}" != "" && params.mode == "plot"){
 	matrix_to_plot = Channel
@@ -203,7 +208,6 @@ if("${params.path_matrix}" != "" && params.mode == "plot"){
 		.map {it -> [it.simpleName, it]}
 }
 
-
 if(params.mode == "uropa"){
 	interaction_uropa = Channel
 		.fromPath("${params.in}/*.normalized.bed")
@@ -235,18 +239,23 @@ if (params.mode != "plot"){
 	}
 
 	if ( "${params.bam}" != "" ){
-		bam_f = Channel
+		Channel
 			.fromPath("${params.bam}/*.bam")
 			.map {it -> [it.simpleName, it]}
+            .into {bam_f; bam_f2}
 		create_bam = false
-	} else {
+	} else if ("${params.mode}" == "HiC" & "${params.mode}" == "h5") {
+        hic_matrix_f = Channel
+                            .fromPath("${params.in}/*.h5")
+                            .map {it -> [it.simpleName, it]}
+    }else {
 		create_bam = true
 		fastqGzFiles = Channel.fromPath("${params.in}/*.fastq*")
 	}
 }
 
-modeList = ["T2C", "HiC", "help", "h", "plot", "uropa", "multiplot"]
-alnList = ["bowtie2", "bwa", "histat"]
+modeList = ["T2C", "HiC", "help", "h", "plot", "uropa", "multiplot", "h5"]
+alnList = ["bowtie2", "bwa"]
 organismList = ["mm10", "mm9", "hg19"]
 
 
@@ -347,45 +356,6 @@ process check_parameters {
 	"""
 }
 
-/*Checks if given Output directory exsists.
-*If it exists it will be deleted or die Pipeline stops. (HiC Mode only)
-*/
-process check_output_directory {
-
-	when:
-	params.mode == 'not_used'
-
-	script:
-	valIn = false
-	if(outfile.exists()){
-		while(!valIn){
-			answer = System.console().readLine 'Output directory "' + outfile + '" already exists: delete directory? (Y/n) \n'
-			if(answer == 'n'){
-				println("WARNING: It is required to delete given directory or choose a differnt directory!\nExiting...")
-				System.exit(0)
-			} else if (answer == 'y' | answer == '') {
-				valIn = true
-				println("Deleting directory...")
-			} else {
-				println("Error: Invalid input!")
-			}
-		}
-	}
-
-	if(valIn){
-		"""
-		if [ -d $outpath ]; then
-			rm -r ${outpath}
-		fi
-		echo 'Check of output directory done'
-		"""
-	} else {
-		"""
-		echo 'Check of output directory done'
-		"""
-	}
-}
-
 /*
 * T2C Step 1
 *Creates restriction maps needed for T2C analysis
@@ -398,7 +368,7 @@ process create_restriction_maps_for_T2C {
 	file ("*.bed") into restriction_maps
 
 	when:
-	params.mode == 'T2C'
+	params.mode == 'T2C' || params.mode == 'multiplot'
 	create_res_map == true
 
 	script:
@@ -432,7 +402,7 @@ process create_restriction_maps_for_T2C {
 	"""
 }
 
-res_map.concat(restriction_maps).into {final_res_map_for_check; final_res_map; final_res_map_for_intersection}
+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 {
@@ -870,6 +840,7 @@ process finish_raw_matrix {
 	output:
 	//set name_raw, file ("${name}.matrix.bed") into raw_matrix_bed_for_plots
 	set name, file ("${name}.matrix.bed") into raw_matrix_bed_to_reassign
+    set name, file ("${name}.matrix.bed") into raw_matrix_for_norm
 
 	when:
 	params.mode == "T2C"
@@ -904,6 +875,7 @@ process	split_matrix_for_re_evaluation {
 
 	when:
 	params.mode == "T2C"
+    params.reassin == 1
 
 	script:
 	"""
@@ -920,6 +892,7 @@ process	split_matrix_for_re_evaluation {
 process intersect_beds_to_fragments {
 
 	tag{name}
+    conda "$workflow.projectDir/envtoucan.yaml"
 
 	if(params.safe_all_files == 1){
 		publishDir "${outpath}/${params.pn}_additional_files/bed/", mode: 'copy'
@@ -933,11 +906,12 @@ process intersect_beds_to_fragments {
 
 	when:
 	params.mode == "T2C"
+    params.reassin == 1
 
 	script:
 	"""
-	sed 's/[[:blank:]]*\$\$//p' ${a_bed} | ${path_bedtools}/bedtools intersect -a ${a_bed} -b ${res_frag} -wao > ${name}.frga.bed
-	sed 's/[[:blank:]]*\$\$//p' ${b_bed} | ${path_bedtools}/bedtools intersect -a ${b_bed} -b ${res_frag} -wao > ${name}.frgb.bed
+	sed 's/[[:blank:]]*\$\$//p' ${a_bed} | bedtools intersect -a ${a_bed} -b ${res_frag} -wao > ${name}.frga.bed
+	sed 's/[[:blank:]]*\$\$//p' ${b_bed} | bedtools intersect -a ${b_bed} -b ${res_frag} -wao > ${name}.frgb.bed
 	"""
 }
 
@@ -961,6 +935,7 @@ process reassign_matrix {
 
 	when:
 	params.mode == "T2C"
+    params.reassin == 1
 
 	script:
 	"""
@@ -990,6 +965,7 @@ process finalize_matrix {
 
 	when:
 	params.mode == "T2C"
+    params.reassin == 1
 
 	script:
 	name_raw =  "${name}_raw"
@@ -1000,6 +976,11 @@ process finalize_matrix {
 	"""
 }
 
+if (params.reassin == 1){
+    matrix = reassigned_matrix
+} else {
+    matrix = raw_matrix_for_norm
+}
 /*
 * T2C step 17
 * Normalize Matrix
@@ -1011,7 +992,7 @@ process normalize_matrix {
 	publishDir "${outpath}/${params.pn}_Interactions/02_all_interactions_bed_norm/", mode: 'copy'
 
 	input:
-	set name, file (matrix) from reassigned_matrix
+	set name, file (matrix) from matrix
 
 	output:
 	set name, file ("${name}.normalized.bed") into normalized_matrix, multiplot_bed_2, filtered_interaction_bed_for_multiplot_2
@@ -1157,8 +1138,8 @@ process create_uropa_config_1 {
                 \\"feature\\" : ${conf_list_final[0]}, \
                 \\"feature.anchor\\" : ${conf_list_final[1]},  \
                 \\"distance\\" : [ \
-                    ${uropa_dist_1}, \
-                    ${uropa_dist_2} \
+                    ${params.uropa_dist_1}, \
+                    ${params.uropa_dist_2} \
                 ], \
                 \\"strand\\" : ${conf_list_final[2]}, \
                 \\"direction\\" : ${conf_list_final[3]}, \
@@ -1255,8 +1236,8 @@ process create_uropa_config_2 {
                 \\"feature\\" : ${conf_list_final[0]}, \
                 \\"feature.anchor\\" : ${conf_list_final[1]},  \
                 \\"distance\\" : [ \
-                    ${uropa_dist_1}, \
-                    ${uropa_dist_2} \
+                    ${params.uropa_dist_1}, \
+                    ${params.uropa_dist_2} \
                 ], \
                 \\"strand\\" : ${conf_list_final[2]}, \
                 \\"direction\\" : ${conf_list_final[3]}, \
@@ -1378,13 +1359,12 @@ process create_viewpoint {
 process convert_to_IFMatrix {
 
 	tag{name}
+    echo true
 
-    if(params.safe_all_files == 1){
-	       publishDir "${outpath}/${params.pn}_additional_files/IFMatrix/", mode: 'copy'
-    }
+	publishDir "${outpath}/${params.pn}_additional_files/IFMatrix/", mode: 'copy'
 
 	input:
-	set name, file (int_bed) from to_ifmatrix
+	set name, file (int_bed), file (res) from to_ifmatrix.combine(res_map_for_ifm.filter{ it.simpleName == "restriction_targets"})
 
 	output:
 	set name, file ("${name}.ifm.txt") into ifmatrix
@@ -1394,7 +1374,7 @@ process convert_to_IFMatrix {
 
 	script:
 	"""
-	${path_R}/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} ${res} ${name}.ifm.txt ${params.chr} ${params.start} ${params.end}
 	"""
 }
 
@@ -1415,20 +1395,23 @@ process run_robusTAD {
 	params.mode == "T2C" || params.mode == "multiplot"
 
 	script:
-	"""
-	${path_R}/Rscript ${path_bin}/bin/RobusTAD.R -i ${tfm} --header FALSE -n norm
-	"""
+    """
+    ${path_R}/Rscript ${path_bin}/bin/RobusTAD.R -i ${tfm} --header FALSE -n norm --minWin 1 --maxWin 500
+    """
 }
+//${path_R}/Rscript ${path_bin}/bin/RobusTAD.R -i ${tfm} --header FALSE -n norm --minWin 1 --maxWin 500
 
 process x_axis_scaling {
 
   tag{name}
 
+  publishDir "${outpath}/${params.pn}_TAD/scaled/", mode: 'copy'
+
   input:
   set name, file (tad) from tadbc
 
   output:
-  set name, file ("${bn}.txt") into tadx, multiplot_TAD
+  set name, file ("${bn}_scaled.txt") into tadx, multiplot_TAD
 
   when:
   params.mode == "T2C" || params.mode == "multiplot"
@@ -1436,7 +1419,7 @@ process x_axis_scaling {
   script:
   bn = tad.baseName
   """
-  ${path_R}/Rscript ${path_bin}/bin/xaxis_scaling.R ${tad} ${params.start} ${params.end} ${bn}.txt
+  ${path_R}/Rscript ${path_bin}/bin/xaxis_scaling.R ${tad} ${params.start} ${params.end} ${bn}_scaled.txt
   """
 }
 
@@ -1525,39 +1508,10 @@ process pptx_writer {
 
 //================================= HiC ========================================
 
-/*
-process create_restriction_maps_for_HiC {
-
-
-	output:
-	file ("rest_site_${params.enzyme_a_name}.bed") into restriction_map_for_hic
-
-	when:
-	params.mode == "HiC"
-
-	script:
-	"""
-	findRestSite --fasta ${path_genome} --searchPattern ${params.enzyme_a_sequence} -o rest_site_${params.enzyme_a_name}.bed
-	"""
-} */
-
-/*
-if(params.aln == "bwa"){
-	bowtie2_alignment = Channel.empty()
-	//histat_alignment = Channel.empty()
-} else if (params.aln == "bowtie2") {
-	//histat_alignment = Channel.empty()
-	bwa_alignment = Channel.empty()
-} else if (params.mode == "histat") {
-	bowtie2_alignment = Channel.empty()
-	bwa_alignment = Channel.empty()
-} */
-
-
 process alignment_with_bwa {
 
 	tag{fastq}
-    publishDir "${outpath}/bam/", mode: 'copy'
+    publishDir "${outpath}/${params.pn}_bam/", mode: 'copy'
     conda "$workflow.projectDir/envtoucan.yaml"
 
 	input:
@@ -1569,13 +1523,14 @@ process alignment_with_bwa {
 
 	when:
 	params.mode == "HiC" && params.aln == "bwa"
+    create_bam == true
 
 	script:
 	"""
 	bwa mem \
 		${params.bwa_HiC_options} \
 		${path_genome} \
-		$fastq | ${path_samtools}/samtools view -Shb > ${fastqName}.bam
+		$fastq | samtools view -Shb > ${fastqName}.bam
 	"""
 }
 
@@ -1586,7 +1541,7 @@ process bowtie2_index {
     conda "$workflow.projectDir/envtoucan.yaml"
 
 	when:
-	params.mode == "HiC" && params.aln == "bowtie2"
+	params.mode == "HiC" && params.aln == "bowtie2" && create_bam == true
 
     output:
     val ("${genome_name}") into index_bt2
@@ -1603,7 +1558,7 @@ process bowtie2_index {
 process alignment_with_bowtie2 {
 
 	tag{fastq}
-    publishDir "${outpath}/bam/", mode: 'copy'
+    publishDir "${outpath}/${params.pn}_bam/", mode: 'copy'
     conda "$workflow.projectDir/envtoucan.yaml"
 
 	input:
@@ -1614,7 +1569,7 @@ process alignment_with_bowtie2 {
 	set basisname, file ("${fastqName}.bam") into bowtie2_alignment
 
 	when:
-	params.mode == "HiC" && params.aln == "bowtie2"
+	params.mode == "HiC" && params.aln == "bowtie2" && create_bam == true
 
 	script:
 	"""
@@ -1623,12 +1578,12 @@ process alignment_with_bowtie2 {
 	"""
 }
 
-hic_alignment = bwa_alignment.concat(bowtie2_alignment) //.concat(histat_alignment)
+hic_alignment = bam_f2.concat(bwa_alignment.concat(bowtie2_alignment)) //.concat(histat_alignment)
 
 process create_HiC_matrix {
 
 	tag{name}
-    publishDir "${outpath}/h5_matrix/", mode: 'copy'
+    publishDir "${outpath}/${params.pn}_h5_matrix/", mode: 'copy'
 
 	input:
 	set name, bams from hic_alignment.groupTuple()
@@ -1664,7 +1619,8 @@ process create_HiC_matrix {
 
 process diagnostic_plot_of_HiC_Matrix {
 
-    publishDir "${outpath}/diagnostic_plots/", mode: 'copy'
+    publishDir "${outpath}/${params.pn}_diagnostic_plots/", mode: 'copy'
+    tag{name}
 
 	input:
 	set name, file (matrix) from hic_matrix_for_diagnostic
@@ -1681,26 +1637,34 @@ process diagnostic_plot_of_HiC_Matrix {
 	"""
 }
 
+hic_matrix_final = hic_matrix_f.concat(hic_matrix)
+
 process correct_matrix {
 
-    publishDir "${outpath}/matrix/", mode: 'copy'
+    tag{name}
+    publishDir "${outpath}/${params.pn}_h5_matrix/", mode: 'copy'
 
     input:
-    set name, file (matrix) from hic_matrix
+    set name, file (matrix) from hic_matrix_final
 
     output:
     set name, file("${name}_corrected.h5") into hic_matrix_corrected
 
+    when:
+    params.mode == "HiC" || params.mode == "h5"
+
     script:
     """
-    hicCorrectMatrix correct -m ${matrix} --filterThreshold ${params.hic_thresh_min} ${params.hic_thresh_max} -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 "${outpath}/plot/", mode: 'copy'
+    tag{name}
+    publishDir "${outpath}/${params.pn}_plot/", mode: 'copy'
 
 	input:
 	set name, file (corrected_matrix) from hic_matrix_corrected
@@ -1712,8 +1676,14 @@ process plot_matrix {
 	params.mode == "HiC"
 
 	script:
-	"""
-	hicPlotMatrix -m ${corrected_matrix} -o ${name}.hic.matrix.png \
-    --dpi 400 --region ${params.chr}:${params.start}-${params.end}
-	"""
+    if ((params.chr != "") && (params.start != 0) && p(arams.end != 0))
+    	"""
+    	hicPlotMatrix -m ${corrected_matrix} -o ${name}.hic.matrix.png \
+        --dpi 400 --region ${params.chr}:${params.start}-${params.end}
+    	"""
+    else
+        """
+        hicPlotMatrix -m ${corrected_matrix} -o ${name}.hic.matrix.png \
+        --dpi 400
+        """
 }
diff --git a/bin/convert_to_IFMatrix.R b/bin/convert_to_IFMatrix.R
index 4e9a9cd..b16cfeb 100644
--- a/bin/convert_to_IFMatrix.R
+++ b/bin/convert_to_IFMatrix.R
@@ -2,23 +2,33 @@
 args = commandArgs(trailingOnly=TRUE)
 
 path_interaction.bed = args[1] #"G://Rene.Wiegandt/01_CHiC/04_results/Pipeline_final_results/MyoG_interaction_bed/I17-1299-02-C2C12_Undiff_MyoG_S10_L001_LN405_001.interactions.bed"
-out = args[2] #"G://Rene.Wiegandt/larp.txt"
+res_map = args[2] #"G://Rene.Wiegandt/01_restriction_maps/restriction_targets.bed"
+out = args[3] #"G://Rene.Wiegandt/larp.txt"
+chr <- args[4]
+start <- args[5]
+end <- args[6]
 
 interaction.bed <- data.table::fread(path_interaction.bed, header = FALSE, sep = "\t")
+map <- data.table::fread(res_map, header = FALSE, sep = "\t")
+
+region_pairs <- subset(map, (V1 == chr & ((start <= V2 & V2 <= end) )))
 
 x <- unique(interaction.bed[,V3])
 y <- unique(interaction.bed[,V6])
 
-bindvec <- sort(unique(as.vector(append(x,y))))
-sizeMatrix <- length(bindvec)
+sizeMatrix <- length(region_pairs$V3)
 
 TADmatrix <- matrix(nrow = sizeMatrix,ncol = sizeMatrix)
-dimnames(TADmatrix) = list(bindvec, bindvec) 
+dimnames(TADmatrix) = list(region_pairs$V3 - 1 , region_pairs$V3 - 1)
 
 for (i in 1:nrow(interaction.bed)) {
   x_name <- as.character(interaction.bed[i,3])
   y_name <- as.character(interaction.bed[i,6])
-  TADmatrix[x_name, y_name ] <- as.double(interaction.bed[i,8])
+  if ((as.numeric(x_name) %in% region_pairs$V3 -1) & (as.numeric(y_name) %in% region_pairs$V3 - 1 )) {
+    TADmatrix[x_name, y_name ] <- as.double(interaction.bed[i,8])
+  } else {
+    TADmatrix[as.character(as.numeric(x_name) + 1), as.character(as.numeric(y_name) + 1) ] <- as.double(interaction.bed[i,8])
+  }
 }
 
 tadFrame <- data.table::data.table(TADmatrix)