From aa874bb15e75bd35fe899ec7afc53203fa991da2 Mon Sep 17 00:00:00 2001
From: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Date: Tue, 7 May 2024 10:22:40 +0200
Subject: [PATCH] Update bcftools merge (#134)

---
 CHANGELOG.md                                  |  2 +-
 modules.json                                  |  3 ++-
 .../bcftools/merge/bcftools-merge.diff        | 25 +++++++++++++++++++
 .../nf-core/bcftools/merge/environment.yml    |  2 +-
 modules/nf-core/bcftools/merge/main.nf        |  4 +--
 5 files changed, 31 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/bcftools/merge/bcftools-merge.diff

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.
 
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..10b5b004
--- /dev/null
+++ b/modules/nf-core/bcftools/merge/bcftools-merge.diff
@@ -0,0 +1,25 @@
+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 @@
+   - 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
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)