add parameter_meta to hisat2 and star

hisat2.wdl

@@ -49,4 +49,20 @@ task Hisat2 {
         cpu: threads + 1
         docker: dockerImage
     }
+
+    parameter_meta {
+        indexFiles: {description: "The hisat2 index files.", category: "required"}
+        inputR1: {description: "The first-/single-end FastQ file.", category: "required"}
+        inputR2: {description: "The second-end FastQ file.", category: "common"}
+        outputBam: {description: "The location the output BAM file should be written to.", category: "required"}
+        sample: {description: "The sample id.", category: "required"}
+        library: {description: "The library id.", category: "required"}
+        readgroup: {description: "The readgroup id.", category: "required"}
+        platform: {description: "The platform used for sequencing.", category: "advanced"}
+        downstreamTranscriptomeAssembly: {description: "Equivalent to hisat2's `--dta` flag.", category: "advanced"}
+        threads: {description: "The number of threads to use.", 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"}
+    }
 }
\ No newline at end of file

star.wdl

@@ -19,7 +19,7 @@ task Star {
         String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
     }
 
-    #TODO Needs to be extended for all possible output extensions
+    #TODO Could be extended for all possible output extensions
     Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
 
     command {
@@ -48,6 +48,24 @@ task Star {
         memory: memory
         docker: dockerImage
     }
+
+    parameter_meta {
+        inputR1: {description: "The first-/single-end FastQ files.", category: "required"}
+        inputR2: {description: "The second-end FastQ files (in the same order as the first-end files).", category: "common"}
+        indexFiles: {description: "The star index files.", category: "required"}
+        outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"}
+        outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"}
+        readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"}
+        outStd: {description: "Equivalent to star's `--outStd` option.", category: "advanced"}
+        twopassMode: {description: "Equivalent to star's `--twopassMode` option.", category: "advanced"}
+        outSAMattrRGline: {description: "The readgroup lines for the fastq pairs given (in the same order as the fastq files).", category: "common"}
+        outSAMunmapped: {description: "Equivalent to star's `--outSAMunmapped` option.", category: "advanced"}
+        limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
+        runThreadN: {description: "The number of threads to use.", 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"}
+    }
 }
 
 task MakeStarRGline {