add parameter_meta to vardict

vardict.wdl

@@ -69,4 +69,34 @@ task VarDict {
         memory: memory
         docker: dockerImage
     }
+
+    parameter_meta {
+        tumorSampleName: {description: "The name of the tumor/case sample.", category: "required"}
+        tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
+        tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
+        normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
+        normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
+        normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
+        referenceFasta: {description: "The reference fasta file.", category: "required"}
+        referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+        bedFile: {description: "A bed file describing the regions to operate on. These regions must be below 1e6 bases in size.", category: "required"}
+        outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
+        chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
+        startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
+        endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
+        geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
+        outputCandidateSomaticOnly: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.", category: "advanced"}
+        outputAllVariantsAtSamePosition: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.", category: "advanced"}
+        mappingQuality: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.", category: "advanced"}
+        minimumTotalDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.", category: "advanced"}
+        minimumVariantDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.", category: "advanced"}
+        minimumAlleleFrequency: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.", category: "advanced"}
+
+        threads: {description: "The number of threads to use.", category: "advanced"}
+        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"}
+    }
 }