[DOC] update README

README.md

@@ -24,9 +24,9 @@ In practice, this workflow was successfully applied to many data-sets including
 dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or
 HiChip data.
 
-Contact maps are generated in standard formats including HiC-Pro, cooler, and h5 format for
+Contact maps are generated in standard formats including HiC-Pro, and cooler for
 downstream analysis and visualization.
-Addition analysis steps such as TADs calling are also available.
+Addition analysis steps such as compartments and TADs calling are also available.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 to run tasks across multiple compute infrastructures in a very portable manner.
@@ -35,15 +35,18 @@ results highly reproducible.
 
 ## Pipeline summary
 
+1. HiC-Pro data processing [`HiC-Pro`](https://github.com/nservant/HiC-Pro)
    1. Mapping using a two steps strategy to rescue reads spanning the ligation
    sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
-2. Detection of valid interaction products([`HiC-Pro`](https://github.com/nservant/HiC-Pro))
+   2. Detection of valid interaction products
    3. Duplicates removal
-4. Create genome-wide contact maps at various resolution ([`cooler`](https://github.com/open2c/cooler))
-5. Contact maps normalization using the ICE algorithm ([`cooler`](https://github.com/open2c/cooler))
-6. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer))
-7. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer))
-8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooler`](https://github.com/open2c/cooler))
+   4. Generate raw and normalized contact maps ([`iced`](https://github.com/hiclib/iced))
+2. Create genome-wide contact maps at various resolution ([`cooler`](https://github.com/open2c/cooler))
+3. Contact maps normalization using balancing algorithm ([`cooler`](https://github.com/open2c/cooler))
+4. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler))
+5. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer))
+6. Compartments calling ([`cooltools`](https://cooltools.readthedocs.io/en/latest/))
+8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
 9. Quality control report ([`MultiQC`](https://multiqc.info/))
 
 ## Quick Start