From 0208430e932282e8c1be0165f56dc121c952c3d6 Mon Sep 17 00:00:00 2001
From: Vitor Heidrich <72625631+vitorheidrich@users.noreply.github.com>
Date: Tue, 30 Apr 2024 15:13:54 +0200
Subject: [PATCH 1/2] Update CHANGELOG.md

---
 CHANGELOG.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 191323f..b10072f 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,13 @@
 ## Version 4.1.1 (Mar 11th, 2024)
 ### Database updates
-* We just released the new vJun23_202403 database
-  * Same SGBs as for the vJun23_202307 version, but the NCBI taxonomy assignment has been fixed to keep the taxa consistent across the MetaPhlAn taxonomic tree
-  * The errors in the relative abundance estimation at higher taxonomic levels had been fixed
-  * Fixed a bug that would halt MetaPhlAn execution when the option `--profile_vsc` was used but had no viral hits
+* We just released the new vJun23_202403 and vOct22_202403 databases
+  * Same SGBs as for the vJun23_202307 and vOct22_202212 versions, respectively, but the NCBI taxonomy assignment has been fixed to keep the taxa consistent across the MetaPhlAn taxonomic tree, allowing accurate relative abundance estimation also at higher taxonomic levels
 ### New features
 * [MetaPhlAn] The new `fix_relab_mpa4.py` script enables to fix errors in the relative abundances in profiles generated with previous databases
 * [MetaPhlAn] Implementation of the option `--subsampling_paired [N_PAIRED_READS]` to subsample paired-end input reads. It needs to be used in conjunction with `-1 [FORWARD_READS_FILE]` and `-2 [REVERSE_READS_FILE]`
+### Fixes
+* Fixed a bug that would halt MetaPhlAn execution when the option `--profile_vsc` was used but had no viral hits
+* Fixed a bug in the new implementation (since StrainPhlAn 4.1) of `–-print_clades_only`
   <br/>
 
 ## Version 4.1.0 (Feb 20th, 2024)
@@ -31,7 +32,7 @@
 * [StrainPhlAn] sample2markers.py output is now in JSON format
 * [StrainPhlAn] Simplified sample and marker filtering parameters, integrated with primary/secondary samples
 * [StrainPhlAn] Faster inference of small and medium phylogenies
-* [StrainPhlAn] Faster execution of the parameter –-print_clades_only
+* [StrainPhlAn] Faster execution of the parameter `–-print_clades_only`
 <br/>
 
 ## Version 4.0.6 (Mar 1st, 2023)

From 1a03e9ee84566ab0b34292de66a89aaeb70845ae Mon Sep 17 00:00:00 2001
From: Vitor Heidrich <72625631+vitorheidrich@users.noreply.github.com>
Date: Wed, 8 May 2024 09:54:28 +0200
Subject: [PATCH 2/2] Update CHANGELOG.md

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b10072f..3da3237 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,8 +6,8 @@
 * [MetaPhlAn] The new `fix_relab_mpa4.py` script enables to fix errors in the relative abundances in profiles generated with previous databases
 * [MetaPhlAn] Implementation of the option `--subsampling_paired [N_PAIRED_READS]` to subsample paired-end input reads. It needs to be used in conjunction with `-1 [FORWARD_READS_FILE]` and `-2 [REVERSE_READS_FILE]`
 ### Fixes
-* Fixed a bug that would halt MetaPhlAn execution when the option `--profile_vsc` was used but had no viral hits
-* Fixed a bug in the new implementation (since StrainPhlAn 4.1) of `–-print_clades_only`
+* [MetaPhlAn] Fixed a bug that would halt MetaPhlAn execution when the option `--profile_vsc` was used but had no viral hits
+* [StrainPhlAn] Fixed a bug in the new implementation (since v4.1) of `–-print_clades_only`
   <br/>
 
 ## Version 4.1.0 (Feb 20th, 2024)