diff --git a/minimap2.wdl b/minimap2.wdl
index d6fa35f67b1306b6fe6dab46264f19631bac8dbd..b4e4d4ee63438570e0512c514565b41f647754fc 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -36,6 +36,7 @@ task Indexing {
     }
 
     command {
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         minimap2 \
         ~{true="-H" false="" useHomopolymerCompressedKmer} \
@@ -92,6 +93,7 @@ task Mapping {
     }
 
     command {
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         minimap2 \
         ~{"-x " + presetOption} \