diff --git a/common.wdl b/common.wdl index 92fd586ce7a9e76572c334faf7e22c6430e910b2..87dcce1391bc938848fee0f551cd230de05af3f5 100644 --- a/common.wdl +++ b/common.wdl @@ -174,6 +174,12 @@ task TextToFile { File out = outputFile } + parameter_meta { + text: {description: "The text to print", category: "required"} + outputFile: {description: "The name of the output file", category: "common"} + 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"} + } runtime { memory: "1G" docker: dockerImage diff --git a/gatk.wdl b/gatk.wdl index b44620aea45bc4be45d4c6a491224bf0a1c85bb9..0b4c71c701b6d7a2ef1013b6ddeef8f77ff6c612 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -342,8 +342,10 @@ task HaplotypeCallerGvcf { parameter_meta { inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"} inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"} - intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"} + intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"} + excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"} gvcfPath: {description: "The location to write the output GVCF to.", category: "required"} + ploidy: {description: "The ploidy with which the variants should be called.", category: "common"} referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"} referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",