Fixed output formatting

docs/output.md

@@ -12,18 +12,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 <!-- no toc -->
 
-- [FASTA and GFF3 validation](#fasta-and-gff3-validation)
-- [Assemblathon stats](#assemblathon-stats)
-- [Genometools gt stat](#genometools-gt-stat)
-- [NCBI FCS adaptor](#ncbi-fcs-adaptor)
-- [NCBI FCS GX](#ncbi-fcs-gx)
-- [BUSCO](#busco)
-- [TIDK](#tidk)
-- [LAI](#lai)
-- [Kraken2](#kraken2)
-- [HiC contact map](#hic-contact-map)
-- [Synteny](#synteny)
-- [Pipeline information](#pipeline-information)
+- [plant-food-research-open/assemblyqc: Output](#plant-food-research-openassemblyqc-output)
+  - [Introduction](#introduction)
+  - [Pipeline overview](#pipeline-overview)
+    - [FASTA and GFF3 validation](#fasta-and-gff3-validation)
+    - [Assemblathon stats](#assemblathon-stats)
+    - [Genometools gt stat](#genometools-gt-stat)
+    - [NCBI FCS adaptor](#ncbi-fcs-adaptor)
+    - [NCBI FCS GX](#ncbi-fcs-gx)
+    - [BUSCO](#busco)
+    - [TIDK](#tidk)
+    - [LAI](#lai)
+    - [Kraken2](#kraken2)
+    - [HiC contact map](#hic-contact-map)
+    - [Synteny](#synteny)
+    - [Pipeline information](#pipeline-information)
 
 ### FASTA and GFF3 validation
 
@@ -56,7 +59,7 @@ The pipeline prints a warning in the pipeline log if FASTA or GFF3 validation fa
 
 GenomeTools `gt stat` tool calculates a basic set of statistics about features contained in GFF3 files.
 
-<div align="center"><figure><img src="images/FI1.gt.stat.yml.gene.length.png" alt="AssemblyQC - GenomeTools gt stat gene length distribution" width="50%"><figure><figcaption>AssemblyQC - GenomeTools gt stat gene length distribution</figcaption></div>
+<div align="center"><figure><img src="images/FI1.gt.stat.yml.gene.length.png" alt="AssemblyQC - GenomeTools gt stat gene length distribution" width="50%"><figcaption>AssemblyQC - GenomeTools gt stat gene length distribution</figcaption><figure></div>
 
 ### NCBI FCS adaptor
 
@@ -86,7 +89,7 @@ GenomeTools `gt stat` tool calculates a basic set of statistics about features c
 
 [BUSCO estimates](https://busco.ezlab.org/busco_userguide.html) the completeness and redundancy of processed genomic data based on universal single-copy orthologs.
 
-<div align="center"><figure><img src="images/busco_figure.png" alt="AssemblyQC - BUSCO summary plot" width="50%"><figure><figcaption>AssemblyQC - BUSCO summary plot</figcaption></div>
+<div align="center"><figure><img src="images/busco_figure.png" alt="AssemblyQC - BUSCO summary plot" width="50%"><figcaption>AssemblyQC - BUSCO summary plot</figcaption><figure></div>
 
 ### TIDK
 
@@ -105,7 +108,7 @@ GenomeTools `gt stat` tool calculates a basic set of statistics about features c
 
 TIDK toolkit is designed to [identify and visualize](https://github.com/tolkit/telomeric-identifier) telomeric repeats for the Darwin Tree of Life genomes.
 
-<div align="center"><figure><img src="images/tidk.png" alt="AssemblyQC - TIDK plot" width="50%"><figure><figcaption>AssemblyQC - TIDK plot</figcaption></div>
+<div align="center"><figure><img src="images/tidk.png" alt="AssemblyQC - TIDK plot" width="50%"><figcaption>AssemblyQC - TIDK plot</figcaption><figure></div>
 
 ### LAI
 
@@ -168,7 +171,7 @@ Hi-C contact mapping experiments measure the frequency of physical contact betwe
 
 Synteny plots are created with Circos which is a tool [facilitating](https://circos.ca) the identification and analysis of similarities and differences arising from comparisons of genomes. The genome-wide alignments are performed with [MUMMER](https://github.com/mummer4/mummer?tab=readme-ov-file) and bundled with [`dnadiff.pl`](https://github.com/mummer4/mummer/blob/master/scripts/dnadiff.pl).
 
-<div align="center"><figure><img src="images/synteny.png" alt="AssemblyQC - Synteny plot" width="50%"><figure><figcaption>AssemblyQC - Synteny plot</figcaption></div>
+<div align="center"><figure><img src="images/synteny.png" alt="AssemblyQC - Synteny plot" width="50%"><figcaption>AssemblyQC - Synteny plot</figcaption><figure></div>
 
 ### Pipeline information