From d78c15e076b4e2a41667c38c9af776f3422f6b9b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 8 Nov 2022 21:21:21 +0100
Subject: [PATCH 1/2] Fix MALT version to 0.61 as this will prevent previously
 borked MALT versions being included in future versions of eager (HOPS does'nt
 pin the MALT version)

---
 environment.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 3f3d30f74..52ba4b254 100644
--- a/environment.yml
+++ b/environment.yml
@@ -43,10 +43,11 @@ dependencies:
   - bioconda::sexdeterrmine=1.1.2
   - bioconda::multivcfanalyzer=0.85.2
   - bioconda::hops=0.35
+  - bioconda::malt=0.61
   - conda-forge::biopython=1.79
   - conda-forge::xopen=1.1.0
   - bioconda::bowtie2=2.4.4
   - bioconda::eigenstratdatabasetools=1.0.2
   - bioconda::mapdamage2=2.2.1
   - bioconda::bbmap=38.92
-  - bioconda::bcftools=1.12
\ No newline at end of file
+  - bioconda::bcftools=1.12

From 116f0e1110b2a9ed3525fd0c47d1663203829c69 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 8 Nov 2022 21:23:12 +0100
Subject: [PATCH 2/2] update MQC and add pinned MALT

---
 CHANGELOG.md    | 3 +++
 environment.yml | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 11917234b..6b6abec41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Dependencies`
 
+- Updated MultiQC to official 1.13 version (rather than alpha)
+- Added pinned MALT dependency to ensure working version in future versions of eager
+
 ### `Deprecated`
 
 ## [2.4.5] - 2022-08-02
diff --git a/environment.yml b/environment.yml
index 52ba4b254..b385a972e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -26,7 +26,7 @@ dependencies:
   - bioconda::qualimap=2.2.2d
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.9 # Don't upgrade - later versions don't allow java 8
-  - bioconda::multiqc=1.13a
+  - bioconda::multiqc=1.13
   - bioconda::pmdtools=0.60
   - bioconda::bedtools=2.30.0
   - conda-forge::libiconv=1.16