[MODIF] update docs

docs/output.md

@@ -9,7 +9,7 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [From raw data to valid pairs]
+- [From raw data to valid pairs](#from-raw-data-to-valid-pairs)
   - [HiC-Pro](#hicpro)
     - [Reads alignment](#reads-alignment)
     - [Valid pairs detection](#valid-pairs-detection)

docs/usage.md

@@ -25,11 +25,9 @@ CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
 CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
 ```
 
-In this case, each sample will be processed as independant chunk and then merge as a single sample to generate the Hi-C contact maps.
-
 ### Full samplesheet
 
-The pipeline is designed to work only with paired-end data. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
+The `nf-core-hic` pipeline is designed to work only with paired-end data. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
 
 ```console
 sample,fastq_1,fastq_2