Merge pull request #1692 from maxulysse/update_VEP

WIP: update VEP to 113.0
nf-core · Oct 24, 2024 · 5c68fda · 5c68fda
2 parents cb535e8 + 689e88a
commit 5c68fda
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Showing 18 changed files with 672 additions and 291 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
 - [1680](https://github.com/nf-core/sarek/pull/1680) - Template update for nf-core/tools v3.0.0
 - [1681](https://github.com/nf-core/sarek/pull/1681) - Template update for nf-core/tools v3.0.1
+- [1692](https://github.com/nf-core/sarek/pull/1692) - Update ensemblvep
 
 ### Fixed
 
@@ -39,7 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Dependency    | Old version | New version |
 | ------------- | ----------- | ----------- |
 | `deepvariant` | 1.5.0       | 1.6.1       |
-| `ensemblvep`  | 111.0       | 112.0       |
+| `ensemblvep`  | 111.0       | 113.0       |
 | `fgbio`       | 2.0.2       | 2.1.2       |
 | `htslib`      | 1.20        | 1.21        |
 | `lofreq`      |             | 2.1.5       |

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -37,7 +37,7 @@ params {
             mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
             ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
             snpeff_db             = 'GRCh37.87'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
         }
@@ -73,7 +73,7 @@ params {
             pon_tbi                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
             sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
             snpeff_db               = 'GRCh38.105'
-            vep_cache_version       = '111'
+            vep_cache_version       = '113'
             vep_genome              = 'GRCh38'
             vep_species             = 'homo_sapiens'
         }
@@ -83,7 +83,7 @@ params {
             ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
             readme                = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
             snpeff_db             = 'GRCh37.87'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
         }
@@ -92,7 +92,7 @@ params {
             fasta                 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
             ngscheckmate_bed      ="${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
             snpeff_db             = 'GRCh38.105'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'GRCh38'
             vep_species           = 'homo_sapiens'
         }
@@ -142,7 +142,7 @@ params {
             bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
             snpeff_db             = 'WBcel235.105'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'WBcel235'
             vep_species           = 'caenorhabditis_elegans'
         }
@@ -208,7 +208,7 @@ params {
             bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
             snpeff_db             = 'R64-1-1.105'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'R64-1-1'
             vep_species           = 'saccharomyces_cerevisiae'
         }
@@ -235,7 +235,7 @@ params {
             bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
             snpeff_db             = 'GRCh38.105'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'GRCh38'
             vep_species           = 'homo_sapiens'
         }
@@ -244,7 +244,7 @@ params {
             fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
             snpeff_db             = 'GRCh37.87'
-            vep_cache_version     = '111'
+            vep_cache_version     = '113'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
         }
@@ -323,7 +323,7 @@ params {
             known_indels_vqsr       = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz'
             ngscheckmate_bed        = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
             snpeff_db               = 'WBcel235.105'
-            vep_cache_version       = '111'
+            vep_cache_version       = '113'
             vep_genome              = 'WBcel235'
             vep_species             = 'caenorhabditis_elegans'
         }

diff --git a/modules.json b/modules.json
@@ -141,12 +141,12 @@
                     },
                     "ensemblvep/download": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules", "vcf_annotate_ensemblvep"]
                     },
                     "fastp": {

diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test