From 91fe9b51386cadf9168156eb35798edf5fb46227 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 17 Sep 2025 10:01:57 +0200
Subject: [PATCH 1/5] bump vep

---
 modules.json                                  |   4 +-
 .../ensemblvep/download/environment.yml       |   7 +-
 modules/nf-core/ensemblvep/download/main.nf   |  22 +-
 modules/nf-core/ensemblvep/download/meta.yml  |  64 ++-
 .../ensemblvep/download/tests/main.nf.test    |   8 +-
 .../download/tests/main.nf.test.snap          | 448 +++++++++---------
 .../ensemblvep/download/tests/nextflow.config |   4 +-
 .../ensemblvep/download/tests/tags.yml        |   2 -
 .../nf-core/ensemblvep/vep/environment.yml    |   7 +-
 modules/nf-core/ensemblvep/vep/main.nf        |  65 +--
 modules/nf-core/ensemblvep/vep/meta.yml       | 140 ++++--
 .../nf-core/ensemblvep/vep/tests/main.nf.test |  58 +--
 .../ensemblvep/vep/tests/main.nf.test.snap    |  22 +-
 .../ensemblvep/vep/tests/nextflow.config      |   9 +-
 modules/nf-core/ensemblvep/vep/tests/tags.yml |   2 -
 15 files changed, 445 insertions(+), 417 deletions(-)
 delete mode 100644 modules/nf-core/ensemblvep/download/tests/tags.yml
 delete mode 100644 modules/nf-core/ensemblvep/vep/tests/tags.yml

diff --git a/modules.json b/modules.json
index dc5a044e..e1a25500 100644
--- a/modules.json
+++ b/modules.json
@@ -53,12 +53,12 @@
                     },
                     "ensemblvep/download": {
                         "branch": "master",
-                        "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831",
+                        "git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
                         "installed_by": ["modules"]
                     },
                     "expansionhunter": {
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
index 2ea8642f..4cb07dc5 100644
--- a/modules/nf-core/ensemblvep/download/environment.yml
+++ b/modules/nf-core/ensemblvep/download/environment.yml
@@ -1,7 +1,8 @@
-name: ensemblvep_download
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::ensembl-vep=111.0
+  # renovate: datasource=conda depName=bioconda/ensembl-vep
+  - bioconda::ensembl-vep=115.1
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
index f9e025a5..36f958f7 100644
--- a/modules/nf-core/ensemblvep/download/main.nf
+++ b/modules/nf-core/ensemblvep/download/main.nf
@@ -1,18 +1,18 @@
 process ENSEMBLVEP_DOWNLOAD {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' :
-        'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/84/8480a9566a1d6162c5119c7ec7e2a9991c6ed4415eabe3b11c728bed2a85b77f/data'
+        : 'community.wave.seqera.io/library/ensembl-vep:115.1--dae34d4b1c5d54d2'}"
 
     input:
     tuple val(meta), val(assembly), val(species), val(cache_version)
 
     output:
     tuple val(meta), path(prefix), emit: cache
-    path "versions.yml"          , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,11 +22,11 @@ process ENSEMBLVEP_DOWNLOAD {
     prefix = task.ext.prefix ?: 'vep_cache'
     """
     vep_install \\
-        --CACHEDIR $prefix \\
-        --SPECIES $species \\
-        --ASSEMBLY $assembly \\
-        --CACHE_VERSION $cache_version \\
-        $args
+        --CACHEDIR ${prefix} \\
+        --SPECIES ${species} \\
+        --ASSEMBLY ${assembly} \\
+        --CACHE_VERSION ${cache_version} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,7 +37,7 @@ process ENSEMBLVEP_DOWNLOAD {
     stub:
     prefix = task.ext.prefix ?: 'vep_cache'
     """
-    mkdir $prefix
+    mkdir ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml
index a4277ad7..df7cf260 100644
--- a/modules/nf-core/ensemblvep/download/meta.yml
+++ b/modules/nf-core/ensemblvep/download/meta.yml
@@ -1,5 +1,6 @@
 name: ensemblvep_download
-description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`.
+description: Ensembl Variant Effect Predictor (VEP). The cache downloading options
+  are controlled through `task.ext.args`.
 keywords:
   - annotation
   - cache
@@ -12,33 +13,44 @@ tools:
       homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
       documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
       licence: ["Apache-2.0"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - assembly:
-      type: string
-      description: |
-        Genome assembly
-  - species:
-      type: string
-      description: |
-        Specie
-  - cache_version:
-      type: string
-      description: |
-        cache version
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - assembly:
+        type: string
+        description: |
+          Genome assembly
+    - species:
+        type: string
+        description: |
+          Specie
+    - cache_version:
+        type: string
+        description: |
+          cache version
 output:
-  - cache:
-      type: file
-      description: cache
-      pattern: "*"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  cache:
+    - - meta:
+          type: file
+          description: cache
+          pattern: "*"
+          ontologies: []
+      - prefix:
+          type: file
+          description: cache
+          pattern: "*"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@maxulysse"
 maintainers:
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test
index 760c9d56..496dbeca 100644
--- a/modules/nf-core/ensemblvep/download/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([
-                    [id:"111_WBcel235"],
+                    [id:"115_WBcel235"],
                     params.vep_genome,
                     params.vep_species,
                     params.vep_cache_version
@@ -26,8 +26,8 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
@@ -41,7 +41,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([
-                    [id:"111_WBcel235"],
+                    [id:"115_WBcel235"],
                     params.vep_genome,
                     params.vep_species,
                     params.vep_cache_version
@@ -51,8 +51,8 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
index 6ea596fb..61234184 100644
--- a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
@@ -5,130 +5,130 @@
                 "0": [
                     [
                         {
-                            "id": "111_WBcel235"
+                            "id": "115_WBcel235"
                         },
                         [
                             [
                                 [
                                     [
-                                        "1-1000000.gz:md5,4da54db2f781d08975630811fd831585",
-                                        "10000001-11000000.gz:md5,7bee73e51d08f5e6de1796614105c5de",
-                                        "1000001-2000000.gz:md5,e8beff9020e261d78988c37e804cc89a",
-                                        "11000001-12000000.gz:md5,1a31b2dcf58822e837cd91b7a74a8b4f",
-                                        "12000001-13000000.gz:md5,34522be2ee5bd3cf51a9b151c877fe35",
-                                        "13000001-14000000.gz:md5,4e5a7b604f8aea2ad9de79b75ed89a6b",
-                                        "14000001-15000000.gz:md5,65146be110ea58b64ab8518bcbfbde9d",
-                                        "15000001-16000000.gz:md5,a39fdb7b0b056c0254574353351722eb",
-                                        "2000001-3000000.gz:md5,b72a04531477615dc4d2c530d09e60df",
-                                        "3000001-4000000.gz:md5,50dae46f370e1468c8f8f2c97cc75f0b",
-                                        "4000001-5000000.gz:md5,e58e124073689212e5311fbd8ccce415",
-                                        "5000001-6000000.gz:md5,db27434dc8be9557f97aa09a95126836",
-                                        "6000001-7000000.gz:md5,a5131e3ee41b329eb55fb3849ddb1471",
-                                        "7000001-8000000.gz:md5,61e1fbe1a82892a0f9f6ee0380fa60bc",
-                                        "8000001-9000000.gz:md5,48166dd4518ec21f597b6acca73809bb",
-                                        "9000001-10000000.gz:md5,3e416c856f40f36ec0ed3f42a93b2267"
+                                        "1-1000000.gz:md5,f9cb33a3ddbb1b82597b3af3e9643dd3",
+                                        "10000001-11000000.gz:md5,71aa93ae6388be95fa5269be60236b95",
+                                        "1000001-2000000.gz:md5,956f858010c1346ee042ef0ea522043b",
+                                        "11000001-12000000.gz:md5,30274a3b8244e492cdf1f611a04848db",
+                                        "12000001-13000000.gz:md5,b28d20155f72c1261ba4bb08bea3d302",
+                                        "13000001-14000000.gz:md5,293a59ed7b397c1817d77412e124df53",
+                                        "14000001-15000000.gz:md5,5291aeb2805c8823b44562d875c7905e",
+                                        "15000001-16000000.gz:md5,7fd86078be5f3a400635b269a02185ea",
+                                        "2000001-3000000.gz:md5,7f6241cf8e3c91e1c882f3cc86d2dc3a",
+                                        "3000001-4000000.gz:md5,e77dc4834119301bbe19dc2a4a05348a",
+                                        "4000001-5000000.gz:md5,ac34c2980fea824b21e04874847904ad",
+                                        "5000001-6000000.gz:md5,3dfdb3bcd812de1e2b69cfca89a1c1f9",
+                                        "6000001-7000000.gz:md5,8446c31796e1aee447af2e353b3734a1",
+                                        "7000001-8000000.gz:md5,f84e88618cf747c774ddb98d971e2615",
+                                        "8000001-9000000.gz:md5,3094317bb21e35067424e9ad957dfcbe",
+                                        "9000001-10000000.gz:md5,3883799cae1ed356ecb416550a89ebde"
                                     ],
                                     [
-                                        "1-1000000.gz:md5,06b83c3bd2c651c5a8a96f0865d54a53",
-                                        "10000001-11000000.gz:md5,79b3348f860370d1697e6d4de128fca3",
-                                        "1000001-2000000.gz:md5,f98e31f3e25c0a419ebeee5b17527b00",
-                                        "11000001-12000000.gz:md5,5f23214fdef1f7637f6046dc751155ed",
-                                        "12000001-13000000.gz:md5,9a4422905679e543a92d47142b1acba1",
-                                        "13000001-14000000.gz:md5,c5db99e7d56f2115f8da8fe3af83314a",
-                                        "14000001-15000000.gz:md5,66b65af3732c0495dc74f3071203ac2f",
-                                        "15000001-16000000.gz:md5,d4c30dc42925cc92dc594d4145544f33",
-                                        "2000001-3000000.gz:md5,ff9b3fd1235468c738e9201e2fa98e08",
-                                        "3000001-4000000.gz:md5,c649308c7d3b4891a8c6f95e583f3a08",
-                                        "4000001-5000000.gz:md5,c53d2fa6695248d0a725ef70325aae91",
-                                        "5000001-6000000.gz:md5,5481fb4b60ebd97256f5d52c42aee0bd",
-                                        "6000001-7000000.gz:md5,94b82e096bacb091e0ef55bcd08b8ab8",
-                                        "7000001-8000000.gz:md5,83f571dfaf8b891bf27208466e6f7d8c",
-                                        "8000001-9000000.gz:md5,4f07e30c7d772544bc6e99bac371b97b",
-                                        "9000001-10000000.gz:md5,f1439765f6428ae99516d95dc5df3926"
+                                        "1-1000000.gz:md5,c2393dd5d120068d496b8789bee91974",
+                                        "10000001-11000000.gz:md5,106ab30775ba5fa950f8df7909a163b2",
+                                        "1000001-2000000.gz:md5,beeda6a82ca6800093d96bbf2eaa81f9",
+                                        "11000001-12000000.gz:md5,27d27c0245dbbb270b2001ca75b03042",
+                                        "12000001-13000000.gz:md5,8eea54682f0ef9e1977527999f6bfe29",
+                                        "13000001-14000000.gz:md5,5f4581505ebf8c4488bff65b16f125e0",
+                                        "14000001-15000000.gz:md5,00e8035d7e179ee51faa7032db090fad",
+                                        "15000001-16000000.gz:md5,c8438ec1765eb98cfca60eb2165f4d70",
+                                        "2000001-3000000.gz:md5,cf3f572db267b4a8552b37d1c3a78b2d",
+                                        "3000001-4000000.gz:md5,ec7df072bf71748c26e25afc2ea353f1",
+                                        "4000001-5000000.gz:md5,9dd91cde9d18bae0c884dff7050abaef",
+                                        "5000001-6000000.gz:md5,1be8b286a79eebb80ff0684f5c110407",
+                                        "6000001-7000000.gz:md5,a0debd5341d3e5ba986225f0f45d01b9",
+                                        "7000001-8000000.gz:md5,fc2d82666540059fea44c14569208b14",
+                                        "8000001-9000000.gz:md5,0a75c0b27da2c4ae946fdae5e5d83e59",
+                                        "9000001-10000000.gz:md5,172900e4145c9a9aa783f01550f4d8a2"
                                     ],
                                     [
-                                        "1-1000000.gz:md5,dab3bbb82e7ecc5430319b7723b88436",
-                                        "10000001-11000000.gz:md5,a1af0b4ce9c2ff301ac0a935a4189c58",
-                                        "1000001-2000000.gz:md5,8a70e4d08b14a4cf19b03a0556a6cae8",
-                                        "11000001-12000000.gz:md5,e866bb880cd79e612dc2081635368017",
-                                        "12000001-13000000.gz:md5,1b5be2ca310afd8289561331d19ddf07",
-                                        "13000001-14000000.gz:md5,907d2bb3f6b9b75fca9e40f1220c0cb4",
-                                        "2000001-3000000.gz:md5,783bcc5957ca4853853c5cda0418dbcd",
-                                        "3000001-4000000.gz:md5,cb2df81caa4a20215bb793ca2a792e01",
-                                        "4000001-5000000.gz:md5,2046030a187c0a86c9be02531aea0ed7",
-                                        "5000001-6000000.gz:md5,395a977401540eb90607b31ecc786a0f",
-                                        "6000001-7000000.gz:md5,e6a97128bc38649fcfa5dcb0032a570e",
-                                        "7000001-8000000.gz:md5,08804df16d4cdeb5a733d2d6b07b058e",
-                                        "8000001-9000000.gz:md5,bba084d260c12613403d144073105d9b",
-                                        "9000001-10000000.gz:md5,c0775c413018ed7964f3042112fe4e26"
+                                        "1-1000000.gz:md5,d1d97f733248a030e650a9bd1e7f41bc",
+                                        "10000001-11000000.gz:md5,429d681ffa8ca9dc23c62cdab4ffc42b",
+                                        "1000001-2000000.gz:md5,58be924f576c85b462df995b76074c9d",
+                                        "11000001-12000000.gz:md5,f789a4312ddd0bd423b3c55f66af782c",
+                                        "12000001-13000000.gz:md5,76a0fdd867ca559eaf5e8fe3e0f8ea94",
+                                        "13000001-14000000.gz:md5,867d9a3b7b6a720b634180efebf65658",
+                                        "2000001-3000000.gz:md5,e93c4b398494843b309abf71b218c14a",
+                                        "3000001-4000000.gz:md5,ff5b0d6680207d23490279c5f62ba33b",
+                                        "4000001-5000000.gz:md5,8b5e33878c599de252a931205a034446",
+                                        "5000001-6000000.gz:md5,25b9f4a4edafb9572c323ca1783dd7c1",
+                                        "6000001-7000000.gz:md5,c52c31d11ab225f7c9793f0c82ce72e6",
+                                        "7000001-8000000.gz:md5,a894863e34285ca3b042cd0eeed253c6",
+                                        "8000001-9000000.gz:md5,bcce1adf098aa44c0e55a2df2d801449",
+                                        "9000001-10000000.gz:md5,b27661dc26cd23c6a9c41cc885187b4f"
                                     ],
                                     [
-                                        "1-1000000.gz:md5,710a2c1ad83c3c9751a0f152cd98f02c",
-                                        "10000001-11000000.gz:md5,ac93a92e62043bddaa59973e26dac8e0",
-                                        "1000001-2000000.gz:md5,232ee5ab6c7295007ffc760f361e4c07",
-                                        "11000001-12000000.gz:md5,07e49ac7b78fbc29cd920b11a4d21afc",
-                                        "12000001-13000000.gz:md5,7849822cf3df022e9f273fb6a928aa8b",
-                                        "13000001-14000000.gz:md5,e3d3f0ee264694c72b3b989a542c5694",
-                                        "14000001-15000000.gz:md5,e5771b6c2fefe9f62b23c71ab873f94f",
-                                        "15000001-16000000.gz:md5,fa02114035f63a504c48005c498f8ec3",
-                                        "16000001-17000000.gz:md5,ef0fd03281afc2e636a64fd61df8c4dc",
-                                        "17000001-18000000.gz:md5,4483a6d74a07b1101dccee71a22213ed",
-                                        "2000001-3000000.gz:md5,f164cbfdc8bc12efd7c26df3935fe190",
-                                        "3000001-4000000.gz:md5,ff05a42801004994a4f30f081bc8945a",
-                                        "4000001-5000000.gz:md5,b63f51d54dc3cb4b214b54527dfa4234",
-                                        "5000001-6000000.gz:md5,6945f59a1fd50f1dfa8a2f1e55fecc12",
-                                        "6000001-7000000.gz:md5,3f27a3cb19ece2a9e87da6fe6476faaa",
-                                        "7000001-8000000.gz:md5,05bffc6e8af7a80fdd6cbc53e5512d0c",
-                                        "8000001-9000000.gz:md5,8a3594ee1eb15d7aa8edeb325e485dce",
-                                        "9000001-10000000.gz:md5,338bce56200690d450d5fcac65a91be7"
+                                        "1-1000000.gz:md5,70dfe9bedc7a87a063f9b6f2e48b846b",
+                                        "10000001-11000000.gz:md5,767a1bd59613ad669cbb835cc11d06ff",
+                                        "1000001-2000000.gz:md5,9e1276159b8a073611f048cf6c4a0738",
+                                        "11000001-12000000.gz:md5,93dcc27f1185c7af20489ce5796da68e",
+                                        "12000001-13000000.gz:md5,0bc55d7b3f7419adcdbf474b7192c5ba",
+                                        "13000001-14000000.gz:md5,2a8c5ee78d9d2b462ec889733f311c19",
+                                        "14000001-15000000.gz:md5,68e79d710886838294c8de27ea7c1c00",
+                                        "15000001-16000000.gz:md5,d975f06bf6f8f1722c29c7b8cce7095b",
+                                        "16000001-17000000.gz:md5,bf59b0b7461b4c97520762754a91e41c",
+                                        "17000001-18000000.gz:md5,3174d1bff1351ee17f632c6adec54c90",
+                                        "2000001-3000000.gz:md5,22ac8f1975b085ed3f5773bc220ff120",
+                                        "3000001-4000000.gz:md5,0a8a89f524f7955f3db2847344e688d9",
+                                        "4000001-5000000.gz:md5,648d45d681cc4cbe68db4638665122ca",
+                                        "5000001-6000000.gz:md5,dfe8c94f45221ed152874083ec0991e2",
+                                        "6000001-7000000.gz:md5,e9c705d31a7c1cac9d02c6a018a0d655",
+                                        "7000001-8000000.gz:md5,723513cca5842d5c238dc110075ad8dd",
+                                        "8000001-9000000.gz:md5,3703d6fbdad1f21a2c1f40c5d8ad5371",
+                                        "9000001-10000000.gz:md5,afb3ba977fc7cd18b47bb5fa6fc85832"
                                     ],
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                                     "info.txt:md5,33ccb74a030a9a345051628c337cb8af"
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@@ -136,135 +136,135 @@
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                                     ],
                                     [
-                                        "1-1000000.gz:md5,267b3134411641d12bb6efcfd5e9d48d",
-                                        "10000001-11000000.gz:md5,4f7473abf622b57ca3c8d6de098759f7",
-                                        "1000001-2000000.gz:md5,5587d56269638b9cc88bdb7ae5dacc58",
-                                        "11000001-12000000.gz:md5,3da928f2caf09b9e3df58f9d1be2c541",
-                                        "12000001-13000000.gz:md5,eae3125082e1674f40fcfb8bb7da23e3",
-                                        "13000001-14000000.gz:md5,6a91eccbe0cf05737e2d2971d5618876",
-                                        "14000001-15000000.gz:md5,60c9b08ad4f674c0394a7c16dee2713e",
-                                        "15000001-16000000.gz:md5,b36c052923f3d3e3cc8db9c2852e1e16",
-                                        "16000001-17000000.gz:md5,0d0d7a8735aadda492912d032fd8733b",
-                                        "17000001-18000000.gz:md5,cf57648ef4cbc3325cff87e6b4b89653",
-                                        "18000001-19000000.gz:md5,5c649205050bfcbb4414db329659dadc",
-                                        "19000001-20000000.gz:md5,48838329ef3e8c26dd8b1ba82f925704",
-                                        "20000001-21000000.gz:md5,c7e1643d2880881fe5d44f718b8e6755",
-                                        "2000001-3000000.gz:md5,94849146caeca44e256aec58f1a914b8",
-                                        "3000001-4000000.gz:md5,4601fbb22fda2cbc4ed397707f8f7afd",
-                                        "4000001-5000000.gz:md5,7c8617d40b6d2e9a37802691f64f775e",
-                                        "5000001-6000000.gz:md5,0e81ba81f807f8429351e46dd8385e0e",
-                                        "6000001-7000000.gz:md5,6e86fccda1dc539e291bd5768ffd0dad",
-                                        "7000001-8000000.gz:md5,f0bf0306012d738fc71f7a26d7af2d81",
-                                        "8000001-9000000.gz:md5,0f3da0d0c714760bc2c39bc6696b74d1",
-                                        "9000001-10000000.gz:md5,4e0e2ba92378f6e1f261d5e59d8e3d9f"
+                                        "1-1000000.gz:md5,ce88865c73633b2b57e6f3481a21b3f8",
+                                        "10000001-11000000.gz:md5,8f1f45979e56451d44a3887321910d30",
+                                        "1000001-2000000.gz:md5,c40b987ac5b22a6674055849e24204ad",
+                                        "11000001-12000000.gz:md5,4e5a2ba329951bd2e01738886766e777",
+                                        "12000001-13000000.gz:md5,0670c5ee8dbf7c5f497a948071f94026",
+                                        "13000001-14000000.gz:md5,24d4532d1e9c0839f750f6dc798beacd",
+                                        "14000001-15000000.gz:md5,3a3de4c21b35ae9cd349e4641d8023a8",
+                                        "15000001-16000000.gz:md5,d60e0088ed511f809d9f2137fe46731c",
+                                        "16000001-17000000.gz:md5,2ee41d67e7cc73cf0e1bf8e47c708436",
+                                        "17000001-18000000.gz:md5,87304db95265191a4368c51ee7993801",
+                                        "18000001-19000000.gz:md5,b943b2b6865fa97a04fac7e17ac7c789",
+                                        "19000001-20000000.gz:md5,4d1338b66252cbc28c9991967cc5805e",
+                                        "20000001-21000000.gz:md5,a81d47d38d78d30bb4575f7a65c9707e",
+                                        "2000001-3000000.gz:md5,2ff7e93b14741df46621a15840fa5276",
+                                        "3000001-4000000.gz:md5,1ff84c0fb7dd85b55a1f32954f3bd625",
+                                        "4000001-5000000.gz:md5,4079a7728625d842f231d1f664b50264",
+                                        "5000001-6000000.gz:md5,399986007f0bc002054aff687bce85fc",
+                                        "6000001-7000000.gz:md5,c97f0d1a323011c5eb59d2c09a12634e",
+                                        "7000001-8000000.gz:md5,0973af953b9632efa1813d0c1265902d",
+                                        "8000001-9000000.gz:md5,1c9695b7857c8494396edbf68e2d8095",
+                                        "9000001-10000000.gz:md5,7e3e78052518c97155260eba1975ec41"
                                     ],
                                     [
-                                        "1-1000000.gz:md5,83a0a200cb053b1f28e41fe62068d49a",
-                                        "10000001-11000000.gz:md5,2f84058256242378b7d14ef526ed42ea",
-                                        "1000001-2000000.gz:md5,c655f70a1d16eef55a5003cdb63434ab",
-                                        "11000001-12000000.gz:md5,6d5c34d7a61fa4764c546d1b46a5c90d",
-                                        "12000001-13000000.gz:md5,84fceee383bb28edb8d749c744a10932",
-                                        "13000001-14000000.gz:md5,aadd01464ca36c813a831f5c2016ba02",
-                                        "14000001-15000000.gz:md5,94a5325ca01192d5eea218b30f933ec4",
-                                        "15000001-16000000.gz:md5,de84954b08d570585a448d8831c12e6d",
-                                        "16000001-17000000.gz:md5,be4954afe2236d62226307f8c9f95820",
-                                        "17000001-18000000.gz:md5,8fdacfb47fc5728eb27b22bbb8c9b301",
-                                        "2000001-3000000.gz:md5,83552c17d88c3986c56c681b0b49bb97",
-                                        "3000001-4000000.gz:md5,deb3bc27c8d431d60fc89a6fe49bcbc6",
-                                        "4000001-5000000.gz:md5,98de5bbb694c73f7ffde16fb92069117",
-                                        "5000001-6000000.gz:md5,7c5a116261bf41309b18c22b0cba5f52",
-                                        "6000001-7000000.gz:md5,fb0d2dc71bd0c9263ff23825d8a4ef64",
-                                        "7000001-8000000.gz:md5,2375dcd7787e7ca5d26442cea0ff6710",
-                                        "8000001-9000000.gz:md5,979f986c27b91a62873e639e3ebeae43",
-                                        "9000001-10000000.gz:md5,b80f6906a724e4b0d6c21dd4c77663fd"
+                                        "1-1000000.gz:md5,e5b943beee3102d4bbcf931618e4516f",
+                                        "10000001-11000000.gz:md5,2258cce59acc40383eba19df4adab977",
+                                        "1000001-2000000.gz:md5,48ffa67b4638d76f54feffeaf3ceb919",
+                                        "11000001-12000000.gz:md5,810e31cc6ef2995163dc4a249c73f131",
+                                        "12000001-13000000.gz:md5,0bf858719d427d5dcff6640dd0126ec0",
+                                        "13000001-14000000.gz:md5,f337fe31c4cf04d2b61c8cc4e65b3d31",
+                                        "14000001-15000000.gz:md5,51fa13d1ceefd98a6a093a41d565aa08",
+                                        "15000001-16000000.gz:md5,eaa3a4f3c8e447a78f482f8ff94ee488",
+                                        "16000001-17000000.gz:md5,95d704615bf688dea4fcf8916ea35326",
+                                        "17000001-18000000.gz:md5,356290a920138412ac131046246fe606",
+                                        "2000001-3000000.gz:md5,b32d23dedc91e0f05047cb3f75ab9679",
+                                        "3000001-4000000.gz:md5,304b9eb63522e575fb97a7c18e602c93",
+                                        "4000001-5000000.gz:md5,d2fa3e7f01321332dc5a65feef9defc0",
+                                        "5000001-6000000.gz:md5,d150eec8b35ccf2e136fdc6e7bd17481",
+                                        "6000001-7000000.gz:md5,fde4ba9ba1cbe463b65afd45f64d0809",
+                                        "7000001-8000000.gz:md5,40a5fe0f827dc040e851c5769896d4f5",
+                                        "8000001-9000000.gz:md5,0112761790ef2e78c5515bb3f9923277",
+                                        "9000001-10000000.gz:md5,f2d25d2a55f146875f0e5d51d3108341"
                                     ],
-                                    "chr_synonyms.txt:md5,8a6fce00cc7817ec727c49b7954f10bc",
+                                    "chr_synonyms.txt:md5,8a7e0941aa4f0e676ab5594f0226b2b5",
                                     "info.txt:md5,33ccb74a030a9a345051628c337cb8af"
                                 ]
                             ]
@@ -272,15 +272,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,954fd177c394ba167d575a6aac47390b"
+                    "versions.yml:md5,b35d817d3e6b1f202b19b4aba779790d"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-04-15T17:20:01.921038"
+        "timestamp": "2025-09-15T20:40:27.688415"
     },
     "celegans - download - stub": {
         "content": [
@@ -288,7 +288,7 @@
                 "0": [
                     [
                         {
-                            "id": "111_WBcel235"
+                            "id": "115_WBcel235"
                         },
                         [
                             
@@ -296,12 +296,12 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,954fd177c394ba167d575a6aac47390b"
+                    "versions.yml:md5,b35d817d3e6b1f202b19b4aba779790d"
                 ],
                 "cache": [
                     [
                         {
-                            "id": "111_WBcel235"
+                            "id": "115_WBcel235"
                         },
                         [
                             
@@ -309,14 +309,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,954fd177c394ba167d575a6aac47390b"
+                    "versions.yml:md5,b35d817d3e6b1f202b19b4aba779790d"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-04-15T18:09:54.909036"
+        "timestamp": "2025-09-15T17:21:33.257963"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config
index 882bce41..882ef8ee 100644
--- a/modules/nf-core/ensemblvep/download/tests/nextflow.config
+++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config
@@ -1,12 +1,12 @@
 params {
-    vep_cache_version   = "111"
+    vep_cache_version   = "115"
     vep_genome          = "WBcel235"
     vep_species         = "caenorhabditis_elegans"
 }
 
 process {
     withName: ENSEMBLVEP_DOWNLOAD {
-        ext.args    = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+        ext.args    = '--AUTO c --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
         ext.prefix  = { "${params.vep_cache_version}_${params.vep_genome}" }
     }
 }
diff --git a/modules/nf-core/ensemblvep/download/tests/tags.yml b/modules/nf-core/ensemblvep/download/tests/tags.yml
deleted file mode 100644
index 26671f3d..00000000
--- a/modules/nf-core/ensemblvep/download/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-ensemblvep/download:
-  - "modules/nf-core/ensemblvep/download/**"
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
index 91457c05..4cb07dc5 100644
--- a/modules/nf-core/ensemblvep/vep/environment.yml
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -1,7 +1,8 @@
-name: ensemblvep_vep
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::ensembl-vep=111.0
+  # renovate: datasource=conda depName=bioconda/ensembl-vep
+  - bioconda::ensembl-vep=115.1
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index e82471aa..b132436b 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -1,70 +1,77 @@
 process ENSEMBLVEP_VEP {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' :
-        'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/84/8480a9566a1d6162c5119c7ec7e2a9991c6ed4415eabe3b11c728bed2a85b77f/data'
+        : 'community.wave.seqera.io/library/ensembl-vep:115.1--dae34d4b1c5d54d2'}"
 
     input:
     tuple val(meta), path(vcf), path(custom_extra_files)
-    val   genome
-    val   species
-    val   cache_version
-    path  cache
+    val genome
+    val species
+    val cache_version
+    path cache
     tuple val(meta2), path(fasta)
-    path  extra_files
+    path extra_files
 
     output:
-    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"              , optional:true, emit: report
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true
+    tuple val(meta), path("*.tab.gz"), emit: tab, optional: true
+    tuple val(meta), path("*.json.gz"), emit: json, optional: true
+    path "*.html", emit: report, optional: true
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
+    def args2 = task.ext.args2 ?: ''
+    def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf'
     def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip'
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
-    def reference = fasta ? "--fasta $fasta" : ""
+    def reference = fasta ? "--fasta ${fasta}" : ""
+    def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : ""
     """
     vep \\
-        -i $vcf \\
+        -i ${vcf} \\
         -o ${prefix}.${file_extension}.gz \\
-        $args \\
-        $compress_cmd \\
-        $reference \\
-        --assembly $genome \\
-        --species $species \\
+        ${args} \\
+        ${compress_cmd} \\
+        ${reference} \\
+        --assembly ${genome} \\
+        --species ${species} \\
         --cache \\
-        --cache_version $cache_version \\
-        --dir_cache $dir_cache \\
-        --fork $task.cpus
+        --cache_version ${cache_version} \\
+        --dir_cache ${dir_cache} \\
+        --fork ${task.cpus}
 
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf'
+    def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : ""
     """
-    echo "" | gzip > ${prefix}.vcf.gz
-    echo "" | gzip > ${prefix}.tab.gz
-    echo "" | gzip > ${prefix}.json.gz
-    touch ${prefix}.summary.html
+    echo "" | gzip > ${prefix}.${file_extension}.gz
+    ${create_index}
+    touch ${prefix}_summary.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml
index d8ff8d14..7d91a7d0 100644
--- a/modules/nf-core/ensemblvep/vep/meta.yml
+++ b/modules/nf-core/ensemblvep/vep/meta.yml
@@ -1,5 +1,6 @@
 name: ensemblvep_vep
-description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
+description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled
+  through `task.ext.args`.
 keywords:
   - annotation
   - vcf
@@ -13,21 +14,24 @@ tools:
       homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
       documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
       licence: ["Apache-2.0"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: |
-        vcf to annotate
-  - custom_extra_files:
-      type: file
-      description: |
-        extra sample-specific files to be used with the `--custom` flag to be configured with ext.args
-        (optional)
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          vcf to annotate
+        ontologies: []
+    - custom_extra_files:
+        type: file
+        description: |
+          extra sample-specific files to be used with the `--custom` flag to be configured with ext.args
+          (optional)
+        ontologies: []
   - genome:
       type: string
       description: |
@@ -44,44 +48,84 @@ input:
       type: file
       description: |
         path to VEP cache (optional)
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing fasta reference information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: |
-        reference FASTA file (optional)
-      pattern: "*.{fasta,fa}"
+      ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing fasta reference information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: |
+          reference FASTA file (optional)
+        pattern: "*.{fasta,fa}"
+        ontologies: []
   - extra_files:
       type: file
       description: |
         path to file(s) needed for plugins  (optional)
+      ontologies: []
 output:
-  - vcf:
-      type: file
-      description: |
-        annotated vcf (optional)
-      pattern: "*.ann.vcf.gz"
-  - tab:
-      type: file
-      description: |
-        tab file with annotated variants (optional)
-      pattern: "*.ann.tab.gz"
-  - json:
-      type: file
-      description: |
-        json file with annotated variants (optional)
-      pattern: "*.ann.json.gz"
-  - report:
-      type: file
-      description: VEP report file
-      pattern: "*.html"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Map with sample information
+      - "*.vcf.gz":
+          type: file
+          description: |
+            annotated vcf (optional)
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  tbi:
+    - - meta:
+          type: map
+          description: |
+            Map with sample information
+      - "*.vcf.gz.tbi":
+          type: file
+          description: |
+            annotated vcf index (optional)
+          pattern: "*.vcf.gz.tbi"
+          ontologies: []
+  tab:
+    - - meta:
+          type: map
+          description: |
+            Map with sample information
+      - "*.tab.gz":
+          type: file
+          description: |
+            tab file with annotated variants (optional)
+          pattern: "*.ann.tab.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  json:
+    - - meta:
+          type: map
+          description: |
+            Map with sample information
+      - "*.json.gz":
+          type: file
+          description: |
+            json file with annotated variants (optional)
+          pattern: "*.ann.json.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  report:
+    - "*.html":
+        type: file
+        description: VEP report file
+        pattern: "*.html"
+        ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@maxulysse"
   - "@matthdsm"
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
index 4aff84a3..b43c3edb 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -9,31 +9,15 @@ nextflow_process {
     tag "modules_nfcore"
     tag "ensemblvep"
     tag "ensemblvep/vep"
-    tag "ensemblvep/download"
 
-    test("test_ensemblvep_vep_fasta_vcf") {
+    test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") {
         config "./vcf.config"
 
-        setup {
-            run("ENSEMBLVEP_DOWNLOAD") {
-                script "../../download/main.nf"
-
-                process {
-                    """
-                    input[0] = Channel.of([
-                        [id:"111_WBcel235"],
-                        params.vep_genome,
-                        params.vep_species,
-                        params.vep_cache_version
-                    ])
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
+                vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect()
+
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
@@ -42,7 +26,7 @@ nextflow_process {
                 input[1] = params.vep_genome
                 input[2] = params.vep_species
                 input[3] = params.vep_cache_version
-                input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
+                input[4] = vep_cache
                 input[5] = Channel.value([
                     [id:"fasta"],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
@@ -53,10 +37,13 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    file(process.out.tbi.get(0).get(1)).name
+                ).match() }
             )
         }
 
@@ -65,26 +52,11 @@ nextflow_process {
     test("test_ensemblvep_vep_fasta_tab_gz") {
         config "./tab.gz.config"
 
-        setup {
-            run("ENSEMBLVEP_DOWNLOAD") {
-                script "../../download/main.nf"
-
-                process {
-                    """
-                    input[0] = Channel.of([
-                        [id:"111_WBcel235"],
-                        params.vep_genome,
-                        params.vep_species,
-                        params.vep_cache_version
-                    ])
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
+                vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect()
+
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
@@ -93,7 +65,7 @@ nextflow_process {
                 input[1] = params.vep_genome
                 input[2] = params.vep_species
                 input[3] = params.vep_cache_version
-                input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
+                input[4] = vep_cache
                 input[5] = Channel.value([
                     [id:"fasta"],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
@@ -104,10 +76,10 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v111.0") }
+                { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.1") }
             )
         }
     }
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
index f937b299..d54754c7 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
@@ -2,25 +2,27 @@
     "test_ensemblvep_vep_fasta_tab_gz": {
         "content": [
             [
-                "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba"
+                "versions.yml:md5,e80fd31af7d8544d38b60e94432e9f3b"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-04-15T17:35:20.694114"
+        "timestamp": "2025-09-15T17:26:00.013731"
     },
-    "test_ensemblvep_vep_fasta_vcf": {
+    "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": {
         "content": [
             [
-                "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba"
-            ]
+                "versions.yml:md5,e80fd31af7d8544d38b60e94432e9f3b"
+            ],
+            "d41d8cd98f00b204e9800998ecf8427e",
+            "test.vcf.gz.tbi"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-04-15T17:34:41.093843"
+        "timestamp": "2025-09-15T17:25:33.689161"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
index 882bce41..8e68fe24 100644
--- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config
+++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
@@ -1,12 +1,5 @@
 params {
-    vep_cache_version   = "111"
+    vep_cache_version   = "115"
     vep_genome          = "WBcel235"
     vep_species         = "caenorhabditis_elegans"
 }
-
-process {
-    withName: ENSEMBLVEP_DOWNLOAD {
-        ext.args    = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
-        ext.prefix  = { "${params.vep_cache_version}_${params.vep_genome}" }
-    }
-}
diff --git a/modules/nf-core/ensemblvep/vep/tests/tags.yml b/modules/nf-core/ensemblvep/vep/tests/tags.yml
deleted file mode 100644
index 4aa4aa45..00000000
--- a/modules/nf-core/ensemblvep/vep/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-ensemblvep/vep:
-  - "modules/nf-core/ensemblvep/vep/**"

From e02ff13587cab24e1a239e951136b8f35202bdc8 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 17 Sep 2025 10:15:01 +0200
Subject: [PATCH 2/5] bump svannotate

---
 modules.json                             |  2 +-
 modules/nf-core/gatk4/svannotate/main.nf | 21 +++++++++++----------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/modules.json b/modules.json
index f816b1a7..6db33464 100644
--- a/modules.json
+++ b/modules.json
@@ -73,7 +73,7 @@
                     },
                     "gatk4/svannotate": {
                         "branch": "master",
-                        "git_sha": "cc7e281e7877146dac79c5a484e6e2b10086234a",
+                        "git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
                         "installed_by": ["modules"]
                     },
                     "gawk": {
diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf
index 5d6f4fed..edb33826 100644
--- a/modules/nf-core/gatk4/svannotate/main.nf
+++ b/modules/nf-core/gatk4/svannotate/main.nf
@@ -1,11 +1,11 @@
 process GATK4_SVANNOTATE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
-        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data'
+        : 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd'}"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(bed), path(non_coding_bed)
@@ -15,9 +15,9 @@ process GATK4_SVANNOTATE {
     tuple val(meta5), path(gtf)
 
     output:
-    tuple val(meta), path("*.vcf.gz")       , emit: vcf
-    tuple val(meta), path("*.vcf.gz.tbi")   , emit: tbi
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("*.vcf.gz"),     emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
+    path "versions.yml",                   emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,9 +33,10 @@ process GATK4_SVANNOTATE {
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[GATK SVAnnotate] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[GATK SVAnnotate] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\

From db4ad619963392c4a7bdc2d11015561340bd4aa2 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 17 Sep 2025 10:16:13 +0200
Subject: [PATCH 3/5] changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 39669d3a..5ec2fff1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 9. Changed the `--annotations_filter` parameter to a `--filter` parameter. This parameter takes an argument of `bcftools filter` to filter the resulting VCFs.
 10. Removed the `--delly_sv_types` parameter.
 11. Moved all `wisecondorx` and `qdnaseq` outputs to a separate directory in each sample output.
+12. Bumped all annotation modules to the latest versions
 
 ### `Fixed`
 

From 8d2e084c8db51b7ba98954278a0d098a83641854 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 17 Sep 2025 12:56:34 +0200
Subject: [PATCH 4/5] latest-everything -> latest-stable

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cf01a50d..fe002881 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,7 +30,7 @@ jobs:
       matrix:
         NXF_VER:
           - "25.04.0"
-          - "latest-everything"
+          - "latest-stable"
         test:
           - "pipeline_sv"
           - "pipeline_cnv"

From 8076b891cac8b84f02bb3bf0f6ec2a6fee0af0cf Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 17 Sep 2025 13:29:30 +0200
Subject: [PATCH 5/5] fix annotation tests

---
 .../main.nf.test.snap                         | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tests/subworkflows/local/vcf_annotate_vep_annotsv/main.nf.test.snap b/tests/subworkflows/local/vcf_annotate_vep_annotsv/main.nf.test.snap
index 0e4dd468..6e1d799e 100644
--- a/tests/subworkflows/local/vcf_annotate_vep_annotsv/main.nf.test.snap
+++ b/tests/subworkflows/local/vcf_annotate_vep_annotsv/main.nf.test.snap
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "reports": [
-                    "test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "vep_vcfs": [
                     [
@@ -45,10 +45,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-10T16:07:52.627675525"
+        "timestamp": "2025-09-17T13:28:06.033331215"
     },
     "homo_sapiens - sv & cnv": {
         "content": [
@@ -92,8 +92,8 @@
                     ]
                 ],
                 "reports": [
-                    "test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                    "test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "test.vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "vep_vcfs": [
                     [
@@ -130,10 +130,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-10T16:08:38.671891243"
+        "timestamp": "2025-09-17T13:29:20.766797749"
     },
     "homo_sapiens - cnv": {
         "content": [
@@ -159,7 +159,7 @@
                     ]
                 ],
                 "reports": [
-                    "test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "vep_vcfs": [
                     [
@@ -181,9 +181,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-10T16:08:11.442901471"
+        "timestamp": "2025-09-17T13:28:25.286369493"
     }
 }
\ No newline at end of file