diff --git a/conf/base.config b/conf/base.config
index c02fe945..c6e21d9c 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -60,4 +60,14 @@ process {
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
+    withName:HISAT2_ALIGN {
+        // Workaround: This step sometimes failes irreproduceably
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
+    withName:CIRIQUANT {
+        // Workaround: This step sometimes failes irreproduceably
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
 }