From 9e3d0afb16836a17f4b72bdbcb914509320df8de Mon Sep 17 00:00:00 2001
From: JP Cartailler <5258731+jpcartailler@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:13:12 -0600
Subject: [PATCH 1/2] Updated CHANGELOG.md as per instructions

---
 CHANGELOG.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 503590cb..efe81e11 100644
--- a/CHANGELOG.md
+++ b/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

From 028f027d85a00b630512ce5f1ff99d0acdfc3b7f Mon Sep 17 00:00:00 2001
From: JP Cartailler <5258731+jpcartailler@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:16:49 -0600
Subject: [PATCH 2/2] Fixed output docs (section 5 and 6 were hidden)

---
 docs/output.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 78f0dcb9..4cf727ef 100644
--- a/docs/output.md
+++ b/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