From 9ba205e825840a6c1fe0928de204c6347d460e5d Mon Sep 17 00:00:00 2001
From: jason-cerrato <45641912+jason-cerrato@users.noreply.github.com>
Date: Wed, 10 Aug 2022 09:00:00 -0400
Subject: [PATCH 1/3] Update "unsorted" to "queryname"

Changed the MergeBamAlignment task to use --SORT_ORDER "queryname" instead of  --SORT_ORDER "unsorted" as this is meant to result in a much more efficient MarkDuplicates task run.

Also updated the file names where "unsorted" was used to use "queryname" instead.
---
 processing-for-variant-discovery-gatk4.wdl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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 \

From 18b73d663e21d6cc866e17f08151a94eb99e4423 Mon Sep 17 00:00:00 2001
From: jason-cerrato <45641912+jason-cerrato@users.noreply.github.com>
Date: Wed, 10 Aug 2022 10:01:42 -0400
Subject: [PATCH 2/3] add ".wdl"

to try and get it working from Dockstore/Terra
---
 .dockstore.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.dockstore.yml b/.dockstore.yml
index 0905fc7..43226b1 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -1,7 +1,7 @@
 
 version: 1.2
 workflows:
-   - name: processing-for-variant-discovery-gatk4
+   - name: processing-for-variant-discovery-gatk4.wdl
      subclass: WDL
      primaryDescriptorPath: /processing-for-variant-discovery-gatk4
      testParameterFiles:

From fa7fba930a461fca63c9d59b99f05a2de56f7d6e Mon Sep 17 00:00:00 2001
From: jason-cerrato <45641912+jason-cerrato@users.noreply.github.com>
Date: Wed, 10 Aug 2022 10:38:47 -0400
Subject: [PATCH 3/3] Update .dockstore.yml

---
 .dockstore.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.dockstore.yml b/.dockstore.yml
index 43226b1..a3d0bbb 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -1,9 +1,9 @@
 
 version: 1.2
 workflows:
-   - name: processing-for-variant-discovery-gatk4.wdl
+   - 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