From 7dd3e4e166d348cd731232f63cbfb51b092150af Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 25 Nov 2024 10:58:35 +0100
Subject: [PATCH] patch vep

---
 modules.json                                     |  3 ++-
 .../nf-core/ensemblvep/vep/ensemblvep-vep.diff   | 16 ++++++++++++++++
 modules/nf-core/ensemblvep/vep/main.nf           |  2 +-
 3 files changed, 19 insertions(+), 2 deletions(-)
 create mode 100644 modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff

diff --git a/modules.json b/modules.json
index 1a2e1206..ba502d28 100644
--- a/modules.json
+++ b/modules.json
@@ -129,7 +129,8 @@
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
                     },
                     "expansionhunter": {
                         "branch": "master",
diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
new file mode 100644
index 00000000..c5a7d13d
--- /dev/null
+++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/ensemblvep/vep'
+'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged
+Changes in 'ensemblvep/vep/main.nf':
+--- modules/nf-core/ensemblvep/vep/main.nf
++++ modules/nf-core/ensemblvep/vep/main.nf
+@@ -20,7 +20,7 @@
+     tuple val(meta), path("*.vcf.gz")  , optional:true, emit: vcf
+     tuple val(meta), path("*.tab.gz")  , optional:true, emit: tab
+     tuple val(meta), path("*.json.gz") , optional:true, emit: json
+-    path "*.summary.html"              , emit: report
++    path "*.summary.html"              , optional:true, emit: report
+     path "versions.yml"                , emit: versions
+ 
+     when:
+
+************************************************************
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index da0e3646..4886b05e 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -20,7 +20,7 @@ process ENSEMBLVEP_VEP {
     tuple val(meta), path("*.vcf.gz")  , optional:true, emit: vcf
     tuple val(meta), path("*.tab.gz")  , optional:true, emit: tab
     tuple val(meta), path("*.json.gz") , optional:true, emit: json
-    path "*.summary.html"              , emit: report
+    path "*.summary.html"              , optional:true, emit: report
     path "versions.yml"                , emit: versions
 
     when: