Merge dev to master

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).
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