readme update

README.md

-# CpG Islands
+# cgi v1.0
 
-Ready to use Nextflow CGI workflow available on genotoul /work/project/lpgp/Nextflow/CGI.
+**cgi** workflow , which agree to FAIR principles , was built in Nexflow dsl2 language, with singularity container for used softwares, optimized in terms of computing resources (cpu, memory), and its use on a informatic farm with a slurm scheduler.
 
-## Usage example
+- CpG islands defined using [EMBOSS newcpgreport](https://www.bioinformatics.nl/cgi-bin/emboss/help/newcpgreport)
+- CpG islands defined using [UCSC cpg_lh](http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1136815349_vADDCkvwSdu3g8CimOykIvSHZHar&db=rn3&c=chr5&g=cpgIsland)
+- window CpG Observed/Expected bases on R script
 
-### newcpgreport
+## Install CGI flow and build singularity image
+
+Clone CGI git and build local singularity image (with system admin rights) based on the provided singularity definition file.
+
+```bash
+git clone https://forgemia.inra.fr/lpgp/cgi.git
+sudo singularity build ./cgi/singularity/CGI.sif ./cgi/singularity/CGI.def
+```
+
+## Usage example ENBOSS newcpgreport
 
 ```bash
 #!/bin/bash
@@ -26,7 +37,7 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 --out_dir "${PWD}/results"
 ```
 
-### cpg_lh (UCSC)
+## Usage example UCSC cpg_lh
 
 ```bash
 #!/bin/bash
@@ -42,7 +53,7 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 --out_dir "${PWD}/results"
 ```
 
-### CpG Obs/Exp window
+## Usage example CpG Obs/Exp slinding windows
 
 ```bash
 #!/bin/bash
@@ -60,11 +71,30 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 --out_dir "${PWD}/results"
 ```
 
-## Install CGI flow and build singularity image
+## Defaults parameters
 
-Clone CGI git and build local singularity image (with system admin) based on the provided singularity definition file.
+Please refer to [EMBOSS newcpgreport](https://www.bioinformatics.nl/cgi-bin/emboss/help/newcpgreport), and [UCSC cpg_lh](http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1136815349_vADDCkvwSdu3g8CimOykIvSHZHar&db=rn3&c=chr5&g=cpgIsland) for complete arguments explanation.
 
 ```bash
-git clone https://forgemia.inra.fr/lpgp/cgi.git
-sudo singularity build ./cgi/singularity/CGI.sif ./cgi/singularity/CGI.def
+# genome input
+genome = false
+
+# newcpgreport options
+newcpgreport = false
+window = 100
+shift = 1
+minlen = 200
+minoe = 0.6
+minpc = 50
+
+# cpg_lh
+cpglh = false
+
+# ObsExp
+obsexp = false
+obsexp_shift = 200
+obsexp_window = 200
+
+# save directory
+out_dir = "${PWD}/results"
 ```