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Update ensemblvep modules (vep, filtervep, download) to 116.1 #12604

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Update ensemblvep modules (vep, filtervep, download) to 116.1 #12604

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3d510b2
update vep to 116.1
ramprasadn Aug 6, 2026
cc743d8
switch to bgzip
ramprasadn Aug 8, 2026
7f892b3
Merge branch 'master' into bumpvep116.1
ramprasadn Aug 9, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/ensemblvep/download/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/download/main.nf
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Expand Up @@ -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)
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4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
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Expand Up @@ -139,7 +139,7 @@
[
"ENSEMBLVEP_DOWNLOAD",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand Down Expand Up @@ -174,7 +174,7 @@
[
"ENSEMBLVEP_DOWNLOAD",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/ensemblvep/filtervep/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/filtervep/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
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Expand Up @@ -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") }
)
}
}
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4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
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Expand Up @@ -6,7 +6,7 @@
[
"ENSEMBLVEP_FILTERVEP",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand All @@ -31,7 +31,7 @@
[
"ENSEMBLVEP_FILTERVEP",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/ensemblvep/vep/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/vep/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/ensemblvep/vep/tests/main.nf.test
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Expand Up @@ -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") }
)
}
}
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
[
"ENSEMBLVEP_VEP",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand Down Expand Up @@ -41,7 +41,7 @@
[
"ENSEMBLVEP_VEP",
"ensemblvep",
"116.0"
"116.1"
]
],
"versions_perlmathcdf": [
Expand Down
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