diff --git a/CHANGELOG.md b/CHANGELOG.md index 49db6bba06ff7aabb706d9c9f9ba58d269bd2fe1..048642605eed6e2a07fea840c9a983e7afdbe8a7 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/multiqc.wdl b/multiqc.wdl index 1c5ecfd49a56ca5efd35ff64f6dfaeae33ca76b1..f30cadeaec3556a6572ef41ddfa9be8b5b05a703 100644 --- a/multiqc.wdl +++ b/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"] + } + } }