bring branch up to date

README.md

@@ -31,11 +31,10 @@ Note: Green shows a value higher than the scale.
 ## Installation and Command-line usage
 ### Dependencies
 * Linux
-* Nextflow version 0.30
+* Nextflow version >= 0.30
 * R version version 3.4.4
   * ggplot2
   * plyr
-  * grid
   * gridExtra
   * gtable
   * RColorBrewer
@@ -48,9 +47,9 @@ Note: Green shows a value higher than the scale.
 * HiCExplorer version 2.1
 * Conda:
   * bowtie2 version 2.3.3.1*
-  * bwa version 0.7*
+  * bwa version 0.7.15*
   * SAMtools version 1.3.1*
-  * BEDtools version 2.27*
+  * BEDtools version 2.27.1*
   * uropa version 2.0.2 alpha*  
 
 ``* Will be implemented automatically through conda enviroment.``
@@ -92,6 +91,7 @@ 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 uropa			   	        - Uropa annoation [T2C]
 	parameters:
@@ -112,6 +112,7 @@ 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:

TOuCAN.nf

@@ -9,7 +9,7 @@ params.safe_all_files = 0
 params.check_res_maps = 0
 params.organism = "mm10"
 params.pn = "Project"
-params.reassin = 0
+params.reassin = 1
 
 // parameter for T2C plots
 params.chr = ""

nextflow.config

@@ -4,8 +4,8 @@ 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 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_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"