Fix for hidden output docs

CHANGELOG.md

@@ -3,6 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [3.2.3] - 2024-XX-XX
+
+### Enhancements
+
+- ...
+
+### Fixes
+
+- Fixed output documentation where sections 5 and 6 of output docs were hidden
+
 ## [3.2.2] - 2024-02-01
 
 ### Enhancements

docs/output.md

@@ -263,7 +263,7 @@ High levels of duplication are not necessarily a problem as long as they are con
   - `.la_dedup.bam`: Coordinate sorted BAM file after Linear Amplification duplicate removal. This is the final post-processed BAM file and so will be saved by default in the results directory.
   - `.la_dedup.bam.bai`: BAI index file for coordinate sorted BAM file after Linear Amplification duplicate removal. This is the final post-processed BAM index file and so will be saved by default in the results directory.
   - `.la_dedup_metrics.txt`: Metrics file from custom deduplication based on read 1 5' start location.
-
+</details>
 In assays where linear amplification is used, the resulting library may contain reads that share the same start site but have a unique 3' end due to random cut and tagmentation with Tn5-ME-B. In this case, these duplicates should be removed by filtering all read 1's based on their 5' start site and keeping the read aligning with the highest mapping quality.
 
 ## 5. <a name='Fragment-basedQC'></a>Fragment-based QC
@@ -345,8 +345,6 @@ MACS2 has its main parameters exposed through the pipeline configuration. The de
 
 ### 6.5. <a name='ConsensusPeaks'></a>Consensus Peaks
 
-</details>
-
 The merge function from [BEDtools](https://github.com/arq5x/bedtools2) is used to merge replicate peaks of the same experimental group to create a consensus peak set. This can then optionally be filtered for consensus peaks contributed to be a threshold number of replicates using `--replicate_threshold`.
 
 ## 7. <a name='Peak-basedQC'></a>Peak-based QC