fix(Manta): bed sort

tasks/Manta.wdl

@@ -21,7 +21,8 @@ task Manta {
     MANTA_ANALYSIS_PATH="/cromwell_root/tmp"
     mkdir -p $MANTA_ANALYSIS_PATH
     
-    cp ${regions} my_baits.bed
+    # Double check: sort the bed file
+    sort -k1,1V -k2,2n -k3,3n ${regions} > my_baits.bed
     bgzip -c my_baits.bed > my_baits.bed.gz
     tabix -p bed my_baits.bed.gz
     # input files