From 79742076d9a129f64a99e1702d6714df00ec8d1f Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 7 May 2024 08:53:10 +0200
Subject: [PATCH 1/4] Update bcftools merge version

---
 modules.json                                       |  3 ++-
 modules/nf-core/bcftools/merge/bcftools-merge.diff | 11 +++++++++++
 modules/nf-core/bcftools/merge/environment.yml     |  2 +-
 3 files changed, 14 insertions(+), 2 deletions(-)
 create mode 100644 modules/nf-core/bcftools/merge/bcftools-merge.diff

diff --git a/modules.json b/modules.json
index 934b44b1..5fb9d3e6 100644
--- a/modules.json
+++ b/modules.json
@@ -18,7 +18,8 @@
                     "bcftools/merge": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bcftools/merge/bcftools-merge.diff"
                     },
                     "bcftools/norm": {
                         "branch": "master",
diff --git a/modules/nf-core/bcftools/merge/bcftools-merge.diff b/modules/nf-core/bcftools/merge/bcftools-merge.diff
new file mode 100644
index 00000000..10132d50
--- /dev/null
+++ b/modules/nf-core/bcftools/merge/bcftools-merge.diff
@@ -0,0 +1,11 @@
+Changes in module 'nf-core/bcftools/merge'
+--- modules/nf-core/bcftools/merge/environment.yml
++++ modules/nf-core/bcftools/merge/environment.yml
+@@ -4,4 +4,4 @@
+   - bioconda
+   - defaults
+ dependencies:
+-  - bioconda::bcftools=1.18
++  - bioconda::bcftools=1.20
+
+************************************************************
diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml
index 55de7cd3..51f1fb75 100644
--- a/modules/nf-core/bcftools/merge/environment.yml
+++ b/modules/nf-core/bcftools/merge/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bcftools=1.18
+  - bioconda::bcftools=1.20

From 47b747f6144cf07ab65dd193b03b5bda13bb7e19 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 7 May 2024 08:53:44 +0200
Subject: [PATCH 2/4] Update bcftools merge version again

---
 modules/nf-core/bcftools/merge/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
index b85d3fec..41dc1a0d 100644
--- a/modules/nf-core/bcftools/merge/main.nf
+++ b/modules/nf-core/bcftools/merge/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
-        'biocontainers/bcftools:1.18--h8b25389_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
+        'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)

From 66fd5da86e9cb5407527240764f2feb83a91c746 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 7 May 2024 08:54:52 +0200
Subject: [PATCH 3/4] Update release date

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a721faf6..6a3d72c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v0.1.0 - [2024-05-06]
+## v0.1.0 - [2024-05-07]
 
 Initial release of genomic-medicine-sweden/nallo, created with the [nf-core](https://nf-co.re/) template.
 

From 6518298b58c6eaed90a57123f8ed68121897c643 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 7 May 2024 09:23:22 +0200
Subject: [PATCH 4/4] fix patch

---
 modules/nf-core/bcftools/merge/bcftools-merge.diff | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/modules/nf-core/bcftools/merge/bcftools-merge.diff b/modules/nf-core/bcftools/merge/bcftools-merge.diff
index 10132d50..10b5b004 100644
--- a/modules/nf-core/bcftools/merge/bcftools-merge.diff
+++ b/modules/nf-core/bcftools/merge/bcftools-merge.diff
@@ -1,4 +1,18 @@
 Changes in module 'nf-core/bcftools/merge'
+--- modules/nf-core/bcftools/merge/main.nf
++++ modules/nf-core/bcftools/merge/main.nf
+@@ -4,8 +4,8 @@
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+-        'biocontainers/bcftools:1.18--h8b25389_0' }"
++        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
++        'biocontainers/bcftools:1.20--h8b25389_0' }"
+ 
+     input:
+     tuple val(meta), path(vcfs), path(tbis)
+
 --- modules/nf-core/bcftools/merge/environment.yml
 +++ modules/nf-core/bcftools/merge/environment.yml
 @@ -4,4 +4,4 @@