add parameter_meta to BWA

bwa.wdl

@@ -42,6 +42,21 @@ task Mem {
         memory: memory
         docker: dockerImage
     }
+
+    parameter_meta {
+        read1: {description: "The first or single end fastq file.", category: "required"}
+        read2: {description: "The second end fastq file.", category: "common"}
+        bwaIndex: {description: "The BWA index files.", category: "required"}
+        outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
+        readgroup: {description: "The readgroup to be assigned to the reads. See BWA mem's `-R` option.", category: "common"}
+
+        threads: {description: "The number of threads to use.", category: "advanced"}
+        memory: {description: "The amount of memory this job will use.", category: "advanced"}
+        picardXmx: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.",
+                  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 Kit {
@@ -91,47 +106,20 @@ task Kit {
     }
 
     parameter_meta {
-        read1: {
-            description: "The first-end fastq file.",
-            category: "required"
-        }
-        read2: {
-            description: "The second-end fastq file.",
-            category: "common"
-        }
-        bwaIndex: {
-            description: "The BWA index, including a .alt file.",
-            category: "required"
-        }
-        outputPrefix: {
-            description: "The prefix of the output files, including any parent directories.",
-            category: "required"
-        }
-        readgroup: {
-            description: "A readgroup identifier.",
-            category: "common"
-        }
-        sixtyFour: {
-            description: "Whether or not the index uses the '.64' suffixes.",
-            category: "common"
-        }
-        threads: {
-            description: "The number of threads to use for alignment.",
-            category: "advanced"
-        }
-        sortThreads: {
-            description: "The number of threads to use for sorting.",
-            category: "advanced"
-        }
-        memory: {
-            description: "The amount of memory this job will use.",
-            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"
-        }
+        # inputs
+        read1: {description: "The first-end fastq file.", category: "required"}
+        read2: {description: "The second-end fastq file.", category: "common"}
+        bwaIndex: {description: "The BWA index, including a .alt file.", category: "required"}
+        outputPrefix: {description: "The prefix of the output files, including any parent directories.", category: "required"}
+        readgroup: {description: "A readgroup identifier.", category: "common"}
+        sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
+        threads: {description: "The number of threads to use for alignment.", category: "advanced"}
+        sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
+        memory: {description: "The amount of memory this job will use.", 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"}
 
+        # outputs
         outputBam: "The produced BAM file."
         outputBamIndex: "The index of the produced BAM file."
     }