Merge pull request nf-core#639 from nf-core/vep_update113

Vep update to 113
genomic-medicine-sweden · Oct 22, 2024 · 610c023 · 610c023
2 parents b2088de + 359d876
commit 610c023
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,17 +29,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Tool updates
 
-| Tool     | Old version | New version |
-| -------- | ----------- | ----------- |
-| bcftools | 1.18        | 1.20        |
-| genmod   | 3.8.2       | 3.8.3       |
-| mosdepth | 0.3.6       | 0.3.8       |
-| multiqc  | 1.21        | 1.25.1      |
-| picard   | 3.1.1       | 3.2.0       |
-| samtools | 1.19.2      | 1.21        |
-| sentieon | 202308.02   | 202308.03   |
-| stranger | 0.8.1       | 0.9.1       |
-| tabix    | 1.19.1      | 1.20        |
+| Tool       | Old version | New version |
+| ---------- | ----------- | ----------- |
+| bcftools   | 1.18        | 1.20        |
+| ensemblvep | 112         | 113         |
+| genmod     | 3.8.2       | 3.8.3       |
+| mosdepth   | 0.3.6       | 0.3.8       |
+| multiqc    | 1.21        | 1.25.1      |
+| picard     | 3.1.1       | 3.2.0       |
+| samtools   | 1.19.2      | 1.21        |
+| sentieon   | 202308.02   | 202308.03   |
+| stranger   | 0.8.1       | 0.9.1       |
+| tabix      | 1.19.1      | 1.20        |
 
 ## 2.2.0 - Dogmatix [2024-09-13]
 

diff --git a/conf/modules/annotate_mobile_elements.config b/conf/modules/annotate_mobile_elements.config
@@ -37,7 +37,7 @@ process {
             '--appris --biotype --buffer_size 100 --canonical --cache --ccds',
             '--compress_output bgzip --distance 5000 --domains',
             '--exclude_predicted --force_overwrite --format vcf',
-            '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged',
+            '--hgvs --humdiv --max_sv_size 248956422 --merged',
             '--no_progress --numbers --per_gene --polyphen p',
             '--protein --offline --regulatory --sift p',
             '--symbol --tsl --uniprot --vcf'

diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config
@@ -29,7 +29,7 @@ process {
             '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz',
             '--distance 0',
             '--buffer_size 20000',
-            '--format vcf --fork 4 --max_sv_size 248956422',
+            '--format vcf --max_sv_size 248956422',
             '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
             '--domains --exclude_predicted --force_overwrite',
             '--hgvs --humdiv --no_progress --numbers',

diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config
@@ -37,13 +37,13 @@ process {
 
     withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV' {
         ext.args = { [
-            '--dir_cache vep_cache',
-            '--dir_plugins vep_cache/Plugins',
+            '--dir_cache cache',
+            '--dir_plugins cache/Plugins',
             '--plugin pLI,pLI_values.txt',
             '--appris --biotype --buffer_size 100 --canonical --cache --ccds',
             '--compress_output bgzip --distance 5000 --domains',
             '--exclude_predicted --force_overwrite --format vcf',
-            '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged',
+            '--hgvs --humdiv --max_sv_size 248956422 --merged',
             '--no_progress --numbers --per_gene --polyphen p',
             '--protein --offline --regulatory --sift p',
             '--symbol --tsl --uniprot --vcf'

diff --git a/modules.json b/modules.json
@@ -123,12 +123,12 @@
                     },
                     "ensemblvep/filtervep": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
                     "expansionhunter": {

diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config