Reset set -e

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} \