comment out healthchecker task and remove duplicate input in bcftools annotate

bcftools.wdl

@@ -44,9 +44,7 @@ task Annotate {
         String? regions
         File? regionsFile
         File? renameChrs
-        File? samplesFile
-        Boolean singleOverlaps = false
-        
+        File? samplesFile        
         
         Int threads = 0
         String memory = "256M"

hmftools.wdl

@@ -269,51 +269,51 @@ task GripssHardFilterApplicationKt {
     }
 }
 
-task HealthChecker {
-    # WIP
-    input {
-        String normalName
-        String tumorName
-
-        String javaXmx = "10G"
-    }
-
-    command {
-        java -Xmx10G \
-        -jar /opt/tools/health-checker/3.1/health-checker.jar \
-        -reference ~{normalName} \
-        -tumor ~{tumorName} \
-        -metrics_dir ~{metricsPath} \
-        -amber_dir ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
-        -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
-        -output_dir ~{outputDir}
-    }
-
-    #    super("health-checker",
-    #             Versions.HEALTH_CHECKER,
-    #             "health-checker.jar",
-    #             "10G",
-    #             Lists.newArrayList("-reference",
-    #                     referenceSampleName,
-    #                     "-tumor",
-    #                     tumorSampleName,
-    #                     "-ref_wgs_metrics_file",
-    #                     referenceMetricsPath,
-    #                     "-tum_wgs_metrics_file",
-    #                     tumorMetricsPath,
-    #                     "-ref_flagstat_file",
-    #                     referenceFlagstatPath,
-    #                     "-tum_flagstat_file",
-    #                     tumorFlagstatPath,
-    #                     "-purple_dir",
-    #                     purplePath,
-    #                     "-output_dir",
-    #                     outputPath));    
-
-    output {
-
-    }
-}
+# task HealthChecker {
+#     # WIP
+#     input {
+#         String normalName
+#         String tumorName
+#
+#         String javaXmx = "10G"
+#     }
+#
+#     command {
+#         java -Xmx10G \
+#         -jar /opt/tools/health-checker/3.1/health-checker.jar \
+#         -reference ~{normalName} \
+#         -tumor ~{tumorName} \
+#         -metrics_dir ~{metricsPath} \
+#         -amber_dir ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
+#         -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
+#         -output_dir ~{outputDir}
+#     }
+#
+#     #    super("health-checker",
+#     #             Versions.HEALTH_CHECKER,
+#     #             "health-checker.jar",
+#     #             "10G",
+#     #             Lists.newArrayList("-reference",
+#     #                     referenceSampleName,
+#     #                     "-tumor",
+#     #                     tumorSampleName,
+#     #                     "-ref_wgs_metrics_file",
+#     #                     referenceMetricsPath,
+#     #                     "-tum_wgs_metrics_file",
+#     #                     tumorMetricsPath,
+#     #                     "-ref_flagstat_file",
+#     #                     referenceFlagstatPath,
+#     #                     "-tum_flagstat_file",
+#     #                     tumorFlagstatPath,
+#     #                     "-purple_dir",
+#     #                     purplePath,
+#     #                     "-output_dir",
+#     #                     outputPath));    
+#
+#     output {
+#
+#     }
+# }
 
 task Purple {
     input {