update hic_dev branche

README.md

@@ -3,7 +3,7 @@
 
 TOuCAN is a Nextflow Pipeline for analysing *Targeted Chromation Capture* (T2C) and *High-throughput Chromatin Capture* (HiC) experiments.
 The basic analysing steps are taken from the [original pipeline](https://www.nature.com/articles/nprot.2017.132) (Petros Kolovos et al.).
-TOuCAN combines these steps to an easy to use pipeline. Furthermore it adds additional features for the analysis.
+TOuCAN combines these steps to an easy to use pipeline. Furthermore, it adds additional features for the analysis.
 
 ## Features
 T2C Analysis:
@@ -52,13 +52,13 @@ Note: Green shows a value higher than the scale.
 * HiCExplorer version 2.1
 
 ### Installation
-To install Nextflow follow the instructions on the offical Nextflow [website](https://www.nextflow.io/).
-After installing all dependencies download TOuCAN from the [TOuCAN GitHub Page](https://github.molgen.mpg.de/loosolab/TOuCAN).
+To install Nextflow, follow the instructions on the offical Nextflow [website](https://www.nextflow.io/).
+After installing all dependencies, download TOuCAN from the [TOuCAN GitHub Page](https://github.molgen.mpg.de/loosolab/TOuCAN).
 Then add all required parameters to the configuration file.
 Please check the following link for detailed information about the [configuraten file setup](https://github.molgen.mpg.de/loosolab/TOuCAN/wiki/How-to-setup-the-TOuCAN-configuration-file).
 
 ### Usage
-To run the pipeline use following command-line:
+To run the pipeline, use following command-line:
 Parameter with default values are optional.
 ```
 Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi] [options]
@@ -125,11 +125,11 @@ After creating the restriction maps write their path into the config file to ski
 creating the restrction maps again. [path_T2C_restriction_maps]
 ```
 ### Input
-HiC and T2C Experiments will result in two fastq files for each sample. A forward and a reversed fastq file. Those files need to have the same basename. To identify those each basename has to end with a 'sample extension'.  
+HiC and T2C Experiments will result in two fastq files for each sample: a forward and a reversed fastq file. Those files need to have the same basename. To identify those, each basename has to end with a 'sample extension'.  
 For example:  
 sample1_R1.fastq  
 sample1_R2.fastq  
-You have to give the extension as a parameter in the commandline or in the configuration file. In this case it would look like this:
+You have to give the extension as a parameter in the commandline or in the configuration file. In this case, it would look like this:
 ```
 params{
 	sample_extension = "_R[12]" // in the configuration file
@@ -138,14 +138,16 @@ params{
 ```
 nextflow run TOuCAN ... --sample_extension _R[12] // as command line parameter
 ```
-## Results
-For a detailed explanation of all Results follow this [link](https://github.molgen.mpg.de/loosolab/TOuCAN/wiki/TOuCAN-Results).
-
 ### Simple Example
 The fastq files are stored in '/example/fastq/'. The target region is on chromosome 1 from base 123000000 to base 125000000.
 The command for the T2C analysis would look like this:
 ```shell
 nextflow run TOuCAN.nf --mode T2C --in /example/fastq/ --out /out/ --chr chr1 --start 123000000 --end 125000000
 ```
 
+## Results
+For a detailed explanation of all Results, follow this [link](https://github.molgen.mpg.de/loosolab/TOuCAN/wiki/TOuCAN-Results).
+
+
+
 

TOuCAN.nf

@@ -50,7 +50,7 @@ log.info """
 
 ==========================================
 
-Usage: nextflow run THCPipe.nf --in [Input Path] --out [Output Path] --mode [Modi] [options]
+Usage: nextflow run TOuCAN.nf --in [Input Path] --out [Output Path] --mode [Modi] [options]
 
 
 --mode help, h					- For showing this help message