add parameter_meta to multiqc

CHANGELOG.md

@@ -11,8 +11,9 @@ that users understand how the changes affect the new version.
 
 version 2.2.0-dev
 ---------------------------
++ Removed unused "verbose" and "quiet" inputs from multiqc.
 + Added parameter_meta sections to a variety of tasks.
-+ Picard's BedToIntervalList outputPath ipnut is now optional (with a default of "regions.interval_list")
++ Picard's BedToIntervalList outputPath input is now optional (with a default of "regions.interval_list")
 + Update htseq to default image version 0.11.2
 + Update biowdl-input-converter in common.wdl to version 0.2.1.
 + Update TALON section to now include the new annotation file output, and add config file creation to the TALON task.

multiqc.wdl

@@ -34,8 +34,6 @@ task MultiQC {
         Boolean megaQCUpload = false # This must be actively enabled in my opinion. The tools default is to upload.
         File? config  # A directory
         String? clConfig
-        Boolean verbose  = false
-        Boolean quiet = false
         Array[Boolean] finished = []  # An array of booleans that can be used to let multiqc wait on stuff.
 
         String memory = "4G"
@@ -92,4 +90,49 @@ task MultiQC {
         memory: memory
         docker: dockerImage
     }
+
+    parameter_meta {
+        analysisDirectory: {description: "The directory to run MultiQC on.", category: "required"}
+        dependencies: {description: "This must be used in order to run multiqc after these tasks.", category: "internal_use_only"}
+        force: {description: "Equivalent to MultiQC's `--force` flag.", category: "advanced"}
+        dirs: {description: "Equivalent to MultiQC's `--dirs` flag.", category: "advanced"}
+        dirsDepth: {description: "Equivalent to MultiQC's `--dirs-depth` option.", category: "advanced"}
+        fullNames: {description: "Equivalent to MultiQC's `--fullnames` flag.", category: "advanced"}
+        title: {description: "Equivalent to MultiQC's `--title` option.", category: "advanced"}
+        comment: {description: "Equivalent to MultiQC's `--comment` option.", category: "advanced"}
+        fileName: {description: "Equivalent to MultiQC's `--filename` option.", category: "advanced"}
+        outDir: {description: "Directory in whihc the output should be written.", category: "common"}
+        template: {description: "Equivalent to MultiQC's `--template` option.", category: "advanced"}
+        tag: {description: "Equivalent to MultiQC's `--tag` option.", category: "advanced"}
+        ignore: {description: "Equivalent to MultiQC's `--ignore` option.", category: "advanced"}
+        ignoreSamples: {description: "Equivalent to MultiQC's `--ignore-samples` option.", category: "advanced"}
+        ignoreSymlinks: {description: "Equivalent to MultiQC's `--ignore-symlinks` flag.", category: "advanced"}
+        sampleNames: {description: "Equivalent to MultiQC's `--sample-names` option.", category: "advanced"}
+        fileList: {description: "Equivalent to MultiQC's `--file-list` option.", category: "advanced"}
+        exclude: {description: "Equivalent to MultiQC's `--exclude` option.", category: "advanced"}
+        module: {description: "Equivalent to MultiQC's `--module` option.", category: "advanced"}
+        dataDir: {description: "Equivalent to MultiQC's `--data-dir` flag.", category: "advanced"}
+        noDataDir: {description: "Equivalent to MultiQC's `--no-data-dir` flag.", category: "advanced"}
+        dataFormat: {description: "Equivalent to MultiQC's `--data-format` option.", category: "advanced"}
+        zipDataDir: {description: "Equivalent to MultiQC's `--zip-data-dir` flag.", category: "advanced"}
+        export: {description: "Equivalent to MultiQC's `--export` flag.", category: "advanced"}
+        flat: {description: "Equivalent to MultiQC's `--flat` flag.", category: "advanced"}
+        interactive: {description: "Equivalent to MultiQC's `--interactive` flag.", category: "advanced"}
+        lint: {description: "Equivalent to MultiQC's `--lint` flag.", category: "advanced"}
+        pdf: {description: "Equivalent to MultiQC's `--pdf` flag.", category: "advanced"}
+        megaQCUpload: {description: "Opposite to MultiQC's `--no-megaqc-upload` flag.", category: "advanced"}
+        config: {description: "Equivalent to MultiQC's `--config` option.", category: "advanced"}
+        clConfig: {description: "Equivalent to MultiQC's `--cl-config` option.", category: "advanced"}
+        finished: {description: "An array of booleans that can be used to let multiqc wait on stuff.", category: "internal_use_only"}
+
+        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"}
+    }
+
+    meta {
+        WDL_AID: {
+            exclude: ["finished", "dependencies"]
+        }
+    }
 }