Update vcf_annotate_snpeff subworkflow

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#2055](https://github.com/nf-core/sarek/pull/2055) - Sort final vcf in varlociraptor sbwfs and update varlociraptor
+- [#2141](https://github.com/nf-core/sarek/pull/2141) - Update snpeff
 
 ### Fixed
 
@@ -23,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency    | Old version | New version |
 | ------------- | ----------- | ----------- |
+| snpeff        | 5.3a        | 5.4a        |
 | varlociraptor | 8.7.4       | 8.9.3       |
 | yte           | 1.9.0       | 1.9.4       |
 
@@ -40,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#2055](https://github.com/nf-core/sarek/pull/2055) - Update varlociraptor to use only one input channel, swap to topics
 - [#2087](https://github.com/nf-core/sarek/pull/2087) - Move parabricks config into its own, adhere to strict syntax, swap to topics
 - [#2139](https://github.com/nf-core/sarek/pull/2139) - Back to dev (3.9.0dev)
+- [#2141](https://github.com/nf-core/sarek/pull/2141) - Update vcf_annotate_snpeff subworkflow, swap tabix/bgziptabix and snpeff to topics, strict syntax
 
 #### Fixed
 

main.nf

@@ -184,8 +184,6 @@ workflow NFCORE_SAREK {
         DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info)
         snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache
         vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map { _meta, cache -> [cache] }
-
-        versions = versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions)
     }
     else {
         // Looks for cache information either locally or on the cloud

modules.json

@@ -508,12 +508,12 @@
                     },
                     "snpeff/download": {
                         "branch": "master",
-                        "git_sha": "b966311b31f51b65e87f124d08f948fec019787d",
+                        "git_sha": "ab50ae0a7c0714bf8b13918c1b7af732002c244d",
                         "installed_by": ["modules"]
                     },
                     "snpeff/snpeff": {
                         "branch": "master",
-                        "git_sha": "b966311b31f51b65e87f124d08f948fec019787d",
+                        "git_sha": "51d2d20973eca80048a9490339e8b421db122908",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
                     "snpsift/annmem": {
@@ -548,7 +548,7 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "f2cfcf9d3f6a2d123e6c44aefa788aa232204a7a",
+                        "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
                     "tabix/tabix": {
@@ -627,7 +627,7 @@
                     },
                     "vcf_annotate_snpeff": {
                         "branch": "master",
-                        "git_sha": "b966311b31f51b65e87f124d08f948fec019787d",
+                        "git_sha": "23004c9c64013c90b7d835621ef4cdeff19a1427",
                         "installed_by": ["subworkflows"]
                     }
                 }