docs: Fix header links in output.md

docs/output.md

@@ -10,27 +10,27 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw and trimmed read QC
 - [FastP](#fastp) - Read trimming
-- [Kraken2](#kraken) - Taxonomic assignment
+- [Kraken2](#kraken2) - Taxonomic assignment
 - [Unicycler](#unicycler) - Short read assembly
-- [Quast](#quast) - Assembly quality score
+- [_Quast_](#quast) - Assembly quality score
 - [Bakta](#bakta) or [_Prokka_](#prokka) - Gene detection and annotation
 - [Panaroo](#panaroo) - Pangenome alignment
 - [MobRecon](#mobrecon) - Reconstruction and typing of plasmids
 - [RGI](#rgi) - Detection and annotation of AMR determinants
 - [IslandPath](#islandpath) - Predicts genomic islands in bacterial and archaeal genomes.
 - [PhiSpy](#phispy) - Prediction of prophages from bacterial genomes
-- [IntegronFinder](#integronfinder) - Finds integrons in DNA sequences
+- [_IntegronFinder_](#integronfinder) - Finds integrons in DNA sequences
 - [Diamond](#diamond) - Detection and annotation of genes using external databases.
-  - [CAZy](#cazy): Carbohydrate metabolism
-  - [VFDB](#vfdb): Virulence factors
-  - [BacMet](#bacmet): Metal resistance determinants
-  - [ICEberg](#iceberg): Integrative and conjugative elements
+  - CAZy: Carbohydrate metabolism
+  - VFDB: Virulence factors
+  - BacMet: Metal resistance determinants
+  - ICEberg: Integrative and conjugative elements
 - [PopPUNK](#poppunk) - Genome clustering
-- [Verticall](#verticall) - Conduct pairwise assembly comparisons between genomes in a same PopPUNK cluster
-- [SKA2](#ska2) - Generate a whole-genome FASTA alignment for each genome within a cluster.
-- [Gubbins](#gubbins) - Detection of recombination events within genomes of the same cluster.
-- [FastTree](#FastTree) or [_IQTree_](#IQTree) - Maximum likelihood core genome phylogenetic tree
-- [_SNPsites_](#SNPsites) - Extracts SNPs from a multi-FASTA alignment
+- [_Verticall_](#verticall) - Conduct pairwise assembly comparisons between genomes in a same PopPUNK cluster
+- [_SKA2_](#ska2) - Generate a whole-genome FASTA alignment for each genome within a cluster.
+- [_Gubbins_](#gubbins) - Detection of recombination events within genomes of the same cluster.
+- [FastTree](#fasttree) or [_IQTree_](#iqtree) - Maximum likelihood core genome phylogenetic tree
+- [_SNPsites_](#snpsites) - Extracts SNPs from a multi-FASTA alignment
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -59,6 +59,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 > **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
 
+### fastp
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `read_processing/fastp/`
+  - `${meta.id}` : Trimmed files and trimming reports for each input sample.
+
+</details>
+
+[fastp](https://github.com/OpenGene/fastp) is a all-in-one fastq preprocessor for read/adapter trimming and quality control. It is used in this pipeline for trimming adapter sequences and discard low-quality reads.
+
 ### Kraken2
 
 <details markdown="1">