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..199acfdf3233 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/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/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/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/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..fa193ada5d8c 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/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/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 bc4bbb28f0c7..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 - - bioconda::htslib=1.21 + # 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..4433eda93689 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/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}" input: tuple val(meta), path(vcf), path(custom_extra_files) 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