(sh_trivial_stats)

New workflow
  * collect SAM flag stats

Author: SHuang-Broad

.dockstore.yml

@@ -138,3 +138,6 @@ workflows:
 - name: VerifyBamFingerprint
   subclass: wdl
   primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/VerifyBamFingerprint.wdl
+- name: CollectBamFlagStats
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CollectBamFlagStats.wdl

wdl/pipelines/TechAgnostic/Utility/CollectBamFlagStats.wdl

@@ -0,0 +1,20 @@
+version 1.0
+
+import "../../../tasks/Utility/BAMutils.wdl" as BU
+
+workflow CollectBamFlagStats {
+    meta {
+        description: "Collect SAM flag stats of an aligned BAM"
+    }
+    input {
+        File bam
+        String disk_type = "HDD"
+    }
+
+    call BU.SamtoolsFlagStats  { input: bam = bam, output_format = 'JSON', disk_type = disk_type }
+    call BU.ParseFlagStatsJson { input: sam_flag_stats_json = SamtoolsFlagStats.flag_stats }
+
+    output {
+        Map[String, Float] sam_flag_stats = ParseFlagStatsJson.qc_pass_reads_SAM_flag_stats
+    }
+}