add parameter_meta to ApplyBQSR, GatherBamFiles and GatherVcfFiles

gatk.wdl

@@ -45,6 +45,25 @@ task ApplyBQSR {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        inputBam: {description: "The BAM file which should be recalibrated.", category: "required"}
+        inputBamIndex: {description: "The input BAM file's index.", category: "required"}
+        outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
+        recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
+        sequenceGroupInterval: {description: "The regions to operate on", category: "advanced"}
+        referenceFasta: {description: "The reference fasta file which was also used for mapping.",
+                         category: "required"}
+        referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+                             category: "required"}
+        referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+
+        memory: {description: "The amount of memory this job will use.", category: "advanced"}
+        javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
+                  category: "advanced"}
+        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+                      category: "advanced"}
+    }
 }
 
 # Generate Base Quality Score Recalibration (BQSR) model

picard.wdl

@@ -322,6 +322,18 @@ task GatherBamFiles {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        inputBams: {description: "The BAM files to be merged together.", category: "required"}
+        inputBamsIndex: {description: "The indexes of the input BAM files.", category: "required"}
+        outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
+
+        memory: {description: "The amount of memory this job will use.", category: "advanced"}
+        javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
+                  category: "advanced"}
+        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+                      category: "advanced"}
+    }
 }
 
 task GatherVcfs {
@@ -352,6 +364,18 @@ task GatherVcfs {
         docker: dockerImage
         memory: memory
     }
+
+    parameter_meta {
+        inputVcfs: {description: "The VCF files to be merged together.", category: "required"}
+        inputVcfIndexes: {description: "The indexes of the input VCF files.", category: "required"}
+        outputVcfPath: {description: "The path where the merged VCF file will be written.", caregory: "required"}
+
+        memory: {description: "The amount of memory this job will use.", category: "advanced"}
+        javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
+                  category: "advanced"}
+        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+                      category: "advanced"}
+    }
 }
 
 # Mark duplicate reads to avoid counting non-independent observations