From 527ca85c2ea9af64d2d7f64498f61a9360d72bab Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 26 Oct 2023 05:43:24 +0200
Subject: [PATCH 1/5] Update MEGAN

---
 modules/nf-core/megan/rma2info/environment.yml | 6 ++++++
 modules/nf-core/megan/rma2info/main.nf         | 6 +++---
 modules/nf-core/megan/rma2info/meta.yml        | 5 ++---
 3 files changed, 11 insertions(+), 6 deletions(-)
 create mode 100644 modules/nf-core/megan/rma2info/environment.yml

diff --git a/modules/nf-core/megan/rma2info/environment.yml b/modules/nf-core/megan/rma2info/environment.yml
new file mode 100644
index 00000000..471e5507
--- /dev/null
+++ b/modules/nf-core/megan/rma2info/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::megan=6.21.7
diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf
index a1f2045a..e91af504 100644
--- a/modules/nf-core/megan/rma2info/main.nf
+++ b/modules/nf-core/megan/rma2info/main.nf
@@ -2,10 +2,10 @@ process MEGAN_RMA2INFO {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::megan=6.21.7"
+    conda 'modules/nf-core/megan/rma2info/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
-        'biocontainers/megan:6.21.7--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/megan:6.24.20--h9ee0642_0':
+        'biocontainers/megan:6.24.20--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(rma6)
diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml
index 710d9346..af3dd96c 100644
--- a/modules/nf-core/megan/rma2info/meta.yml
+++ b/modules/nf-core/megan/rma2info/meta.yml
@@ -13,7 +13,6 @@ tools:
       tool_dev_url: "https://github.com/husonlab/megan-ce"
       doi: "10.1371/journal.pcbi.1004957"
       licence: "['GPL >=3']"
-
 input:
   - meta:
       type: map
@@ -27,7 +26,6 @@ input:
   - megan_summary:
       type: boolean
       description: Specify whether to generate an MEGAN summary file
-
 output:
   - meta:
       type: map
@@ -46,6 +44,7 @@ output:
       type: file
       description: Optionally generated MEGAN summary file
       pattern: "*.megan"
-
 authors:
   - "@jfy133"
+maintainers:
+  - "@jfy133"

From 06d4360541eb92b14b85f7e5c293b6968b85ac8f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 26 Oct 2023 05:45:56 +0200
Subject: [PATCH 2/5] Update CHANGELOG

---
 CHANGELOG.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ffd9c45..7eac5e3b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,10 +12,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
-- [#406] Fixed overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#409] Fix a null pointer exception error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
 
 ### `Dependencies`
 
+| Tool           | Previous version | New version |
+| -------------- | ---------------- | ----------- |
+| megan/rma2info | 6.21.7           | 6.24.20     |
+
 ### `Deprecated`
 
 ## v1.1.1 - Augmented Akita Patch [2023-10-11]

From aa4e9162f2567b4a30a8fb19a1846d418bfbd80f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 26 Oct 2023 05:46:48 +0200
Subject: [PATCH 3/5] Update Changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7eac5e3b..e1c13b4b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
 - [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
-- [#409] Fix a null pointer exception error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
 
 ### `Dependencies`
 

From 19865202a0077f3b351d2ebc8953a25430a9ec69 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 26 Oct 2023 05:47:32 +0200
Subject: [PATCH 4/5] Add PR links in CHANGELOG

---
 CHANGELOG.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e1c13b4b..c8bc3b12 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,13 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#408] Added preprint citation information to README and manifest (added by @jfy133)
+- [#408](https://github.com/nf-core/taxprofiler/pull/408) Added preprint citation information to README and manifest (added by @jfy133)
 
 ### `Fixed`
 
-- [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
-- [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
-- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#405](https://github.com/nf-core/taxprofiler/pull/405) Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#406](https://github.com/nf-core/taxprofiler/pull/406) Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#409](https://github.com/nf-core/taxprofiler/pull/409) Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
 
 ### `Dependencies`
 

From c22f719be45faa27c70cba324d74c1f915ef8149 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 26 Oct 2023 06:01:52 +0200
Subject: [PATCH 5/5] Add missing modules.json update

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 9dc77080..aa63d31d 100644
--- a/modules.json
+++ b/modules.json
@@ -163,7 +163,7 @@
                     },
                     "megan/rma2info": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "dbce8951ff9a39ad08d87e563636bbcc6ef34032",
                         "installed_by": ["modules"]
                     },
                     "metaphlan/mergemetaphlantables": {