From 3d510b21d26c2a6ccb4a6d2004dd346355fc9eda Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 6 Aug 2026 14:28:32 +0200
Subject: [PATCH 1/2] update vep to 116.1

---
 modules/nf-core/ensemblvep/download/environment.yml          | 2 +-
 modules/nf-core/ensemblvep/download/main.nf                  | 4 ++--
 modules/nf-core/ensemblvep/download/tests/main.nf.test.snap  | 4 ++--
 modules/nf-core/ensemblvep/filtervep/environment.yml         | 2 +-
 modules/nf-core/ensemblvep/filtervep/main.nf                 | 4 ++--
 modules/nf-core/ensemblvep/filtervep/tests/main.nf.test      | 2 +-
 modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap | 4 ++--
 modules/nf-core/ensemblvep/vep/environment.yml               | 2 +-
 modules/nf-core/ensemblvep/vep/main.nf                       | 4 ++--
 modules/nf-core/ensemblvep/vep/tests/main.nf.test            | 2 +-
 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap       | 4 ++--
 11 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
index 3d904beca05a..adcb42936b9a 100644
--- a/modules/nf-core/ensemblvep/download/environment.yml
+++ b/modules/nf-core/ensemblvep/download/environment.yml
@@ -5,7 +5,7 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/ensembl-vep
-  - bioconda::ensembl-vep=116.0
+  - bioconda::ensembl-vep=116.1
   # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
   # renovate: datasource=conda depName=bioconda/htslib
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
index 1f7c19a3f3dc..27e08ead3b57 100644
--- a/modules/nf-core/ensemblvep/download/main.nf
+++ b/modules/nf-core/ensemblvep/download/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/112b7b57f93b053ccd3f8b2f2207a5faa629fd4ea181af8e1a41a1fbd007e657/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:c4edd3fb4a233ae6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/42/42395bfb0f82afd646493f279327c792d76ce8458ae4907cf00aa8d18f697955/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:037b358ef2f4ce79'}"
 
     input:
     tuple val(meta), val(assembly), val(species), val(cache_version)
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 7f47772a6d83..6ad5d9a0c35e 100644
--- a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
@@ -139,7 +139,7 @@
                     [
                         "ENSEMBLVEP_DOWNLOAD",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [
@@ -174,7 +174,7 @@
                     [
                         "ENSEMBLVEP_DOWNLOAD",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [
diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
index 3d904beca05a..adcb42936b9a 100644
--- a/modules/nf-core/ensemblvep/filtervep/environment.yml
+++ b/modules/nf-core/ensemblvep/filtervep/environment.yml
@@ -5,7 +5,7 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/ensembl-vep
-  - bioconda::ensembl-vep=116.0
+  - bioconda::ensembl-vep=116.1
   # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
   # renovate: datasource=conda depName=bioconda/htslib
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
index 16e8eb037b6b..ebfb67f0eaee 100644
--- a/modules/nf-core/ensemblvep/filtervep/main.nf
+++ b/modules/nf-core/ensemblvep/filtervep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/112b7b57f93b053ccd3f8b2f2207a5faa629fd4ea181af8e1a41a1fbd007e657/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:c4edd3fb4a233ae6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/42/42395bfb0f82afd646493f279327c792d76ce8458ae4907cf00aa8d18f697955/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:037b358ef2f4ce79'}"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
index 1019a799a56f..92fa0d980e1e 100644
--- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
@@ -110,7 +110,7 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() },
-                { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v116.0") }
+                { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v116.1") }
             )
         }
     }
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
index 7246f84aea09..db7f4a968523 100644
--- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
@@ -6,7 +6,7 @@
                     [
                         "ENSEMBLVEP_FILTERVEP",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [
@@ -31,7 +31,7 @@
                     [
                         "ENSEMBLVEP_FILTERVEP",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
index 3d904beca05a..adcb42936b9a 100644
--- a/modules/nf-core/ensemblvep/vep/environment.yml
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -5,7 +5,7 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/ensembl-vep
-  - bioconda::ensembl-vep=116.0
+  - bioconda::ensembl-vep=116.1
   # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
   # renovate: datasource=conda depName=bioconda/htslib
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index 914bc9293247..a41df0e63c08 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/112b7b57f93b053ccd3f8b2f2207a5faa629fd4ea181af8e1a41a1fbd007e657/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:c4edd3fb4a233ae6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/42/42395bfb0f82afd646493f279327c792d76ce8458ae4907cf00aa8d18f697955/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:037b358ef2f4ce79'}"
 
     input:
     tuple val(meta), path(vcf), path(custom_extra_files)
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
index ea6d9acc37b0..454b79d948b1 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -88,7 +88,7 @@ nextflow_process {
                     file(process.out.tab[0][1]).name,
                     process.out.findAll { key, val -> key.startsWith("versions")
                 }).match() },
-                { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v116.0") }
+                { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v116.1") }
             )
         }
     }
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 5d7229772e79..7acbc48c1fcd 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                     [
                         "ENSEMBLVEP_VEP",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [
@@ -41,7 +41,7 @@
                     [
                         "ENSEMBLVEP_VEP",
                         "ensemblvep",
-                        "116.0"
+                        "116.1"
                     ]
                 ],
                 "versions_perlmathcdf": [

From cc743d8b0fb3f99a6e3bc4539e7a07c4954fe563 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Sat, 8 Aug 2026 11:07:54 +0200
Subject: [PATCH 2/2] switch to bgzip

---
 modules/nf-core/ensemblvep/vep/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index a41df0e63c08..ca91cb274304 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -60,7 +60,7 @@ process ENSEMBLVEP_VEP {
     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 > ${prefix}.${file_extension}.gz
+    echo "" | bgzip > ${prefix}.${file_extension}.gz
     ${create_index}
     touch ${prefix}_summary.html
     """