diff --git a/README.md b/README.md index 65f10a0..2a455a8 100644 --- a/README.md +++ b/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 @@ -138,9 +138,6 @@ 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: @@ -148,4 +145,9 @@ The command for the T2C analysis would look like this: 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). + + + diff --git a/TOuCAN.nf b/TOuCAN.nf index 063b0f2..812f73a 100644 --- a/TOuCAN.nf +++ b/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