diff --git a/CHANGELOG.md b/CHANGELOG.md index 11f39da52d..6797e4bb50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -62,6 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage - [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally - [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0` +- [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module ### Fixed diff --git a/conf/igenomes.config b/conf/igenomes.config index b960797e5e..6634ef8cb5 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -29,7 +29,7 @@ params { mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem" snpeff_db = 'GRCh37.75' snpeff_genome = 'GRCh37' - vep_cache_version = 104 + vep_cache_version = 105 vep_genome = 'GRCh37' vep_species = 'homo_sapiens' } @@ -55,7 +55,7 @@ params { pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi" snpeff_db = 'GRCh38.99' snpeff_genome = 'GRCh38' - vep_cache_version = 104 + vep_cache_version = 105 vep_genome = 'GRCh38' vep_species = 'homo_sapiens' } @@ -107,7 +107,7 @@ params { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" snpeff_db = 'WBcel235.99' snpeff_genome = 'WBcel235' - vep_cache_version = 104 + vep_cache_version = 105 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' } diff --git a/modules.json b/modules.json index 5f69191ce0..0c330b13f3 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "ensemblvep": { - "git_sha": "30f72e24822576c6f90a0bf9db678b403c70eccf" + "git_sha": "757c20c8ebfab85e1de9f98773a2269f6d34025a" }, "fastqc": { "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" diff --git a/modules/nf-core/modules/ensemblvep/main.nf b/modules/nf-core/modules/ensemblvep/main.nf index 391a182def..d9bd3e831f 100644 --- a/modules/nf-core/modules/ensemblvep/main.nf +++ b/modules/nf-core/modules/ensemblvep/main.nf @@ -2,10 +2,10 @@ process ENSEMBLVEP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) + conda (params.enable_conda ? "bioconda::ensembl-vep=105.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' : - 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : + 'quay.io/biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" input: tuple val(meta), path(vcf)