Bump Severus to 1.3 (#557)

* Bump Severus version * Update CHANGELOG.md
genomic-medicine-sweden · Feb 12, 2025 · c0d7c7f · c0d7c7f
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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
 - [#541](https://github.com/genomic-medicine-sweden/nallo/pull/541) - Updated template to nf-core/tools version 3.1.2
 - [#545](https://github.com/genomic-medicine-sweden/nallo/pull/545) - Changed CI to use `latest-stable` version of Nextflow instead of `latest-everything`
 - [#556](https://github.com/genomic-medicine-sweden/nallo/pull/556) - Changed family-level SNVs naming to `snvs` from `snv`, matching sample-level and other variants
+- [#557](https://github.com/genomic-medicine-sweden/nallo/pull/557) - Updated Severus to version 1.3
 - [#558](https://github.com/genomic-medicine-sweden/nallo/pull/558) - Changed VEP to single-threaded by default, because of https://github.com/Ensembl/ensembl-vep/issues/1759
 
 ### `Removed`
@@ -53,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | paraphase      | 3.1.1       | 3.2.1       |
 | bcftools merge |             | 1.20        |
 | merge_json     |             | 1.0         |
+| severus        | 1.1         | 1.3         |
 
 > [!NOTE]
 > Version has been updated if both old and new version information is present.

diff --git a/modules.json b/modules.json
@@ -234,7 +234,7 @@
                     },
                     "severus": {
                         "branch": "master",
-                        "git_sha": "8a36181859504560ef333c299f6773c7b99a801f",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "sniffles": {

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