From f163371958423c5dce6cc0e078c16a8e35d2fc6d Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Wed, 4 Jan 2023 17:06:05 +0100
Subject: [PATCH] [MODIF] update docs
---
docs/output.md | 2 +-
docs/usage.md | 4 +---
2 files changed, 2 insertions(+), 4 deletions(-)
diff --git a/docs/output.md b/docs/output.md
index 5839983..4595abf 100644
--- a/docs/output.md
+++ b/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)
diff --git a/docs/usage.md b/docs/usage.md
index 3b2dbb4..961766c 100644
--- a/docs/usage.md
+++ b/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
--
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