From c9ea4ed1228355ae8356e5d80369b28a20ba2179 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 27 May 2026 09:08:53 +0200 Subject: [PATCH 1/4] Add htslib dependency to environment.yml --- modules/nf-core/ensemblvep/vep/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 7e60f7f954b0..6f21c2b2c010 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -6,3 +6,4 @@ channels: dependencies: - bioconda::ensembl-vep=115.2 - bioconda::perl-math-cdf=0.1 + - bioconda::htslib=1.23.1 From f7282f9629d3c526b5b0cbabd3e8e64cdf9e6b6a Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 27 May 2026 09:30:57 +0200 Subject: [PATCH 2/4] bump htslib pin for ensemblvep --- modules/nf-core/ensemblvep/download/environment.yml | 4 ++++ modules/nf-core/ensemblvep/download/main.nf | 4 ++-- modules/nf-core/ensemblvep/filtervep/environment.yml | 4 ++++ modules/nf-core/ensemblvep/filtervep/main.nf | 4 ++-- modules/nf-core/ensemblvep/vep/environment.yml | 3 +++ modules/nf-core/ensemblvep/vep/main.nf | 4 ++-- 6 files changed, 17 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index 7e60f7f954b0..48fc515c72bd 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -4,5 +4,9 @@ channels: - conda-forge - bioconda dependencies: + # renovate: datasource=conda depName=bioconda/ensembl-vep - bioconda::ensembl-vep=115.2 + # renovate: datasource=conda depName=bioconda/perl-math-cdf - bioconda::perl-math-cdf=0.1 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.23.1 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index bc88281f7579..4a1a60b73321 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/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: tuple val(meta), val(assembly), val(species), val(cache_version) diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 7e60f7f954b0..48fc515c72bd 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -4,5 +4,9 @@ channels: - conda-forge - bioconda dependencies: + # renovate: datasource=conda depName=bioconda/ensembl-vep - bioconda::ensembl-vep=115.2 + # renovate: datasource=conda depName=bioconda/perl-math-cdf - bioconda::perl-math-cdf=0.1 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.23.1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index ac9f33cc02ff..f298b5360b67 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/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: tuple val(meta), path(input) diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 6f21c2b2c010..48fc515c72bd 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -4,6 +4,9 @@ channels: - conda-forge - bioconda dependencies: + # renovate: datasource=conda depName=bioconda/ensembl-vep - bioconda::ensembl-vep=115.2 + # renovate: datasource=conda depName=bioconda/perl-math-cdf - bioconda::perl-math-cdf=0.1 + # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.23.1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index b51f641ea89b..d057e869ca38 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/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: tuple val(meta), path(vcf), path(custom_extra_files) From a71ed9181ab0cec431c9c315d06fbd23a54fae81 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 27 May 2026 09:46:15 +0200 Subject: [PATCH 3/4] fix snapshots --- .../ensemblvep/download/tests/main.nf.test.snap | 10 +++++----- .../ensemblvep/vep/tests/main.nf.test.snap | 16 ++++++++-------- .../tests/main.nf.test.snap | 8 ++++---- 3 files changed, 17 insertions(+), 17 deletions(-) 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 9ceb840a0c68..e5618485afe7 100644 --- a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap @@ -151,11 +151,11 @@ ] } ], + "timestamp": "2026-02-13T13:36:59.060515944", "meta": { "nf-test": "0.9.4", "nextflow": "26.01.1" - }, - "timestamp": "2026-02-13T13:36:59.060515944" + } }, "ENSEMBLVEP download cache for 115_WBcel235 - stub": { "content": [ @@ -166,7 +166,7 @@ "id": "115_WBcel235" }, [ - + ] ] ], @@ -186,10 +186,10 @@ ] } ], + "timestamp": "2026-02-13T13:37:10.696285488", "meta": { "nf-test": "0.9.4", "nextflow": "26.01.1" - }, - "timestamp": "2026-02-13T13:37:10.696285488" + } } } \ No newline at end of file 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 6f834d3ecf91..1c0f9c6b8d21 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -21,15 +21,15 @@ [ "ENSEMBLVEP_VEP", "tabix", - "1.21" + "1.23.1" ] ] } ], - "timestamp": "2026-02-06T12:47:57.03116265", + "timestamp": "2026-05-27T09:34:16.339141", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.5", + "nextflow": "26.04.2" } }, "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { @@ -55,15 +55,15 @@ [ "ENSEMBLVEP_VEP", "tabix", - "1.21" + "1.23.1" ] ] } ], - "timestamp": "2026-02-06T12:47:34.421995264", + "timestamp": "2026-05-27T09:33:53.016807", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.5", + "nextflow": "26.04.2" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap index d66f2a16b413..06d92bf572e9 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap @@ -21,11 +21,11 @@ ] ] ], + "timestamp": "2026-01-20T10:44:55.042159577", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T10:44:55.042159577" + } }, "WBcel235 caenorhabditis_elegans 115 - test.vcf.gz - stub": { "content": [ @@ -49,10 +49,10 @@ ] ] ], + "timestamp": "2026-01-20T10:45:05.801478657", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T10:45:05.801478657" + } } } \ No newline at end of file From 5b101e75b252e8c6adb361840ed288bfe9064804 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 27 May 2026 09:53:37 +0200 Subject: [PATCH 4/4] fix singularity container --- modules/nf-core/ensemblvep/download/main.nf | 2 +- modules/nf-core/ensemblvep/filtervep/main.nf | 2 +- modules/nf-core/ensemblvep/vep/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index 4a1a60b73321..199acfdf3233 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -4,7 +4,7 @@ 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/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data' : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index f298b5360b67..fa193ada5d8c 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -4,7 +4,7 @@ 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/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data' : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index d057e869ca38..4433eda93689 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,7 +4,7 @@ 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/sha256/44/44136fa355b3678a1146ad16f7e8649e94fb4fc21fe77e8310c060f61caaff8a/data' + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data' : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: