Final adjustments to 3.1.0 Release

.github/workflows/nf-test.yml

@@ -68,7 +68,8 @@ jobs:
       fail-fast: false
       matrix:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
-        profile: [conda, docker, singularity]
+        # Add conda to once conda lock file support is added
+        profile: [docker, singularity]
         isMain:
           - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         # Exclude conda and singularity on dev

CHANGELOG.md

@@ -57,6 +57,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Template update 3.2.1 [#369](https://github.com/nf-core/mhcquant/pull/369)
 - Bump OpenMS version 3.1.0 -> 3.4.0 [#370](https://github.com/nf-core/mhcquant/pull/358)
 
+### `Changed`
+
+- Temporarily drop conda and epicore testing due to unstable CI tests [#426](https://github.com/nf-core/mhcquant/pull/426)
+
 ### `Dependencies`
 
 | Dependency            | Old version | New version |

docs/usage.md

@@ -159,6 +159,9 @@ This approach is particularly useful when creating reference libraries for subse
 
 ## Epicore
 
+> [!NOTE]
+> This tool is still experimental and under active development.
+
 Length variants of HLA peptides, especially HLA class II peptides, pose a distinct challenge when performing downstream cohort-wide analyses. [Epicore](https://github.com/AG-Walz/epicore) uses rules-based parameters to aggregate length variants of the same epitope into a `consensus epitope`.
 
 Run epicore in the pipeline: