Merge template updates up to 2.14.1

CHANGELOG.md

@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Update to nf-core template `2.14.1`
 - [#237](https://github.com/nf-core/epitopeprediction/pull/237) - Update to nf-core template `2.13.1`
 
+### `Fixed`
+
+- [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Add check for protein map to prevent failure if no information is available
+
 ## v2.3.0 - Oesterberg - 2024-02-26
 
 ### `Changed`

bin/epaa.py

@@ -425,6 +425,11 @@ def read_lig_ID_values(filename):
 
 def create_protein_column_value(pep):
     # retrieve Ensembl protein ID for given transcript IDs, if we want to provide additional protein ID types, adapt here
+
+    # we have to catch cases where no protein information is available, e.g. if there are issues on BioMart side
+    if transcriptProteinTable is None:
+        return ""
+
     all_proteins = [
         # split by : otherwise epytope generator suffix included
         transcriptProteinTable.query(f'transcript_id == "{transcript.transcript_id.split(":")[0]}"')["ensembl_id"]