diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 3fb244fe73795317cc151baacff998f13bc9f985..e5f90e0e42aeaf8b574a9a2dcda27f6e651b4886 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -36,7 +36,7 @@ SOFTWARE_REGEX = {
     'BDBag': ['version_bdbag.txt', r"BDBag (\S+) \(Bagit \S+\)"],
     'RSeQC': ['version_rseqc.txt', r"infer_experiment.py (\S+)"],
     'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
-    'HISAT2': ['version_hisat.txt', r".* version (\S+)"],
+    'HISAT2': ['version_hisat2.txt', r"version (\S+)"],
     'Samtools': ['version_samtools.txt', r"samtools (\S+)"],
     'picard (MarkDuplicates)': ['version_markdups.txt', r"Version: (\S+)"],
     'featureCounts': ['version_featurecounts.txt', r"featureCounts v(\S+)"],