diff --git a/.dockstore.yml b/.dockstore.yml
index 0905fc7..a3d0bbb 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -3,7 +3,7 @@ version: 1.2
 workflows:
    - name: processing-for-variant-discovery-gatk4
      subclass: WDL
-     primaryDescriptorPath: /processing-for-variant-discovery-gatk4
+     primaryDescriptorPath: /processing-for-variant-discovery-gatk4.wdl
      testParameterFiles:
      -  /processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json
      -  /processing-for-variant-discovery-gatk4.b37.wgs.inputs.json
diff --git a/processing-for-variant-discovery-gatk4.wdl b/processing-for-variant-discovery-gatk4.wdl
index 91e62f9..d0d0da8 100644
--- a/processing-for-variant-discovery-gatk4.wdl
+++ b/processing-for-variant-discovery-gatk4.wdl
@@ -124,7 +124,7 @@ workflow PreProcessingForVariantDiscovery_GATK4 {
         bwa_commandline = bwa_commandline,
         bwa_version = GetBwaVersion.version,
         aligned_bam = SamToFastqAndBwaMem.output_bam,
-        output_bam_basename = bam_basename + ".aligned.unsorted",
+        output_bam_basename = bam_basename + ".aligned.queryname",
         ref_fasta = ref_fasta,
         ref_fasta_index = ref_fasta_index,
         ref_dict = ref_dict,
@@ -142,7 +142,7 @@ workflow PreProcessingForVariantDiscovery_GATK4 {
   call MarkDuplicates {
     input:
       input_bams = MergeBamAlignment.output_bam,
-      output_bam_basename = base_file_name + ".aligned.unsorted.duplicates_marked",
+      output_bam_basename = base_file_name + ".aligned.queryname.duplicates_marked",
       metrics_filename = base_file_name + ".duplicate_metrics",
       docker_image = gatk_docker,
       gatk_path = gatk_path,
@@ -376,7 +376,7 @@ task MergeBamAlignment {
       --OUTPUT ~{output_bam_basename}.bam \
       --REFERENCE_SEQUENCE ~{ref_fasta} \
       --PAIRED_RUN true \
-      --SORT_ORDER "unsorted" \
+      --SORT_ORDER "queryname" \
       --IS_BISULFITE_SEQUENCE false \
       --ALIGNED_READS_ONLY false \
       --CLIP_ADAPTERS false \