diff --git a/docs/usage.md b/docs/usage.md
index a742d128..66d0b357 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -10,24 +10,24 @@ Table of contents:
   - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data)
     - [Updating the pipeline](#updating-the-pipeline)
   - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data)
-      - [Samplesheet](#samplesheet)
-      - [Reference files and parameters](#reference-files-and-parameters)
-        - [1. Alignment](#1-alignment)
-        - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files)
-        - [3. Repeat expansions](#3-repeat-expansions)
-        - [4. Variant calling - SNV](#4-variant-calling---snv)
-        - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants)
-        - [6. Copy number variant calling](#6-copy-number-variant-calling)
-        - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking)
-        - [8. SV annotation \& Ranking](#8-sv-annotation--ranking)
-        - [9. Mitochondrial annotation](#9-mitochondrial-annotation)
-        - [10. Mobile element calling](#10-mobile-element-calling)
-        - [11. Mobile element annotation](#11-mobile-element-annotation)
-        - [12. Variant evaluation](#12-variant-evaluation)
-        - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens)
-      - [Run the pipeline](#run-the-pipeline)
-        - [Direct input in CLI](#direct-input-in-cli)
-        - [Import from a config file (recommended)](#import-from-a-config-file-recommended)
+    - [Samplesheet](#samplesheet)
+    - [Reference files and parameters](#reference-files-and-parameters)
+      - [1. Alignment](#1-alignment)
+      - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files)
+      - [3. Repeat expansions](#3-repeat-expansions)
+      - [4. Variant calling - SNV](#4-variant-calling---snv)
+      - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants)
+      - [6. Copy number variant calling](#6-copy-number-variant-calling)
+      - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking)
+      - [8. SV annotation \& Ranking](#8-sv-annotation--ranking)
+      - [9. Mitochondrial annotation](#9-mitochondrial-annotation)
+      - [10. Mobile element calling](#10-mobile-element-calling)
+      - [11. Mobile element annotation](#11-mobile-element-annotation)
+      - [12. Variant evaluation](#12-variant-evaluation)
+      - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens)
+    - [Run the pipeline](#run-the-pipeline)
+      - [Direct input in CLI](#direct-input-in-cli)
+      - [Import from a config file (recommended)](#import-from-a-config-file-recommended)
   - [Best practices](#best-practices)
   - [Core Nextflow arguments](#core-nextflow-arguments)
     - [`-profile`](#-profile)