Bump annotation module versions (#119)

* bump vep

* bump svannotate

* changelog

* latest-everything -> latest-stable

* fix annotation tests

Author: nvnieuwk

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
       matrix:
         NXF_VER:
           - "25.04.0"
-          - "latest-everything"
+          - "latest-stable"
         test:
           - "pipeline_sv"
           - "pipeline_cnv"

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 9. Changed the `--annotations_filter` parameter to a `--filter` parameter. This parameter takes an argument of `bcftools filter` to filter the resulting VCFs.
 10. Removed the `--delly_sv_types` parameter.
 11. Moved all `wisecondorx` and `qdnaseq` outputs to a separate directory in each sample output.
+12. Bumped all annotation modules to the latest versions
 
 ### `Fixed`
 

modules.json

@@ -53,12 +53,12 @@
                     },
                     "ensemblvep/download": {
                         "branch": "master",
-                        "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831",
+                        "git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
                         "installed_by": ["modules"]
                     },
                     "expansionhunter": {
@@ -73,7 +73,7 @@
                     },
                     "gatk4/svannotate": {
                         "branch": "master",
-                        "git_sha": "cc7e281e7877146dac79c5a484e6e2b10086234a",
+                        "git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
                         "installed_by": ["modules"]
                     },
                     "gawk": {