Beginning of Readme redaction

README.md

-# nextflow pipeline
+# ChIPster
 
-This repository is a template and a library repository to help you build nextflow pipeline.
-You can fork this repository to build your own pipeline.
+ChIPster is a nextflow pipeline dedicated to analyse ChIPseq data. 
 
 ## Getting the last updates
 
 To get the last commits from this repository into your fork use the following commands:
 
-For the first time:
 ```sh
-git remote add upstream git@gitbio.ens-lyon.fr:pipelines/nextflow.git
-git pull upstream master
-```
-
-Then to make an update:
-```sh
-git pull upstream master
-git merge upstream/master
+git clone git@gitbio.ens-lyon.fr:xgrand/ChIPster.git
 ```
 
 ## Getting Started
 
-These instructions will get you a copy of the project as a template when you want to build your own pipeline.
-
-[you can follow them here.](doc/getting_started.md)
-
-## Building your pipeline
-
-You can follow the [building your pipeline guide](./doc/building_your_pipeline.md) for a gentle introduction to `nextflow` and taking advantage of this template to build your pipelines.
-
-## Existing Nextflow pipeline
-
-Before starting a new project, you can check if someone else didn’t already to the work !
-- [on the nextflow project page](./doc/nf_projects.md)
-- [on the nf-core project](https://nf-co.re/pipelines)
+The pipeline `src/chipster.nf` works with a configuration file in **Yaml** containing experiment information and a nextflow configuration file `src/nextflow.config`.
+
+The arguments of this pipeline are described in the table below:
+
+|         Arguments           |                             Description                             | 
+|:---------------------------:|:-------------------------------------------------------------------:| 
+| -c | configuration file. This parameter should always be `src/nextflow.config`        | 
+| -profile      | The profile to use. This can be **docker** or **singularity** to run the pipeline in docker or singularity container respectively. This can also be **psmn** to launch the analysis on the PSMN | 
+| -params-file      |  A **yaml** configuration file containing experiement information required for analysis | 
+
+The composition of **Yaml** parameters file is described in the following table:
+
+|         Arguments           |                             Description                             | 
+|:---------------------------:|:-------------------------------------------------------------------:| 
+| paired_end | Boolean to setup sequencing type (paired-end or single-end), default = false | 
+| fastq_folder | Directory containing fastq files (rawdata) | 
+| genome | Path to the reference genome fasta file | 
+| genome_size | Entire genome size (hg19 = 2913022398) |
+| chrom_sizes | A file containing chromosome sizes (usualy "chrom.sizes" file) |
+| idx | Directory containing previously indexed genome files with bowtie2 or "" (empty string to perform the indexation during the pipeline analysis) |
+| project | Project name to prefix results directories and files |
+| input | Balise of input data |
+| row<n> | Corresponds to the balise of the n sample |
+| sample | Sample must be a string. It corresponds to the name of the sample |
+| fastq | The corresponding fastq file, can be compressed as gz file |
+| condition | Condition name, must be the same for IP and Input corresponding samples |
+| type | "IP" or "Input" corresponding to sample type |
 
 ## Contributing
 
@@ -41,9 +46,8 @@ If you want to add more tools to this project, please read the [CONTRIBUTING.md]
 
 ## Authors
 
-* **Laurent Modolo** - *Initial work*
-
-See also the list of [contributors](https://gitbio.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
+* **Xavier Grand** - *Maintainer*
+* **Laurent Modolo** - *template work*
 
 ## License