Fixed names

gatk.wdl

@@ -40,12 +40,11 @@ task ApplyBQSR {
     }
 
     output {
-        IndexedBamFile recalibrated_bam = {
+        IndexedBamFile recalibratedBam = {
             "file": outputBamPath,
-            "index": sub(outputBamPath, "\.bam$", ".bai")
+            "index": sub(outputBamPath, "\.bam$", ".bai"),
+            "md5": outputBamPath + ".md5"
         }
-
-        File recalibrated_bam_checksum = outputBamPath + ".md5"
     }
 
     runtime {

picard.wdl

@@ -204,6 +204,7 @@ task GatherBamFiles {
     input {
         String? preCommand
         Array[File]+ inputBams
+        Array[File]+ inputBamsIndex
         String outputBamPath
         String? picardJar