diff --git a/bwa.wdl b/bwa.wdl index e4f1e12dabda7f31adf778c47d9daf3e728f48e4..b1079cf2a35e21069a133c383dc01b6f073b7e41 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -89,6 +89,52 @@ task Kit { memory: memory docker: dockerImage } + + parameter_meta { + read1: { + description: "The first-end fastq file.", + category: "required" + } + read2: { + description: "The second-end fastq file.", + category: "common" + } + bwaIndex: { + description: "The BWA index, including a .alt file.", + category: "required" + } + outputPrefix: { + description: "The prefix of the output files, including any parent directories", + category: "required" + } + readgroup: { + description: "A readgroup identifier.", + category: "common" + } + sixtyFour: { + description: "Whether or not the index uses the '.64' suffixes.", + category: "common" + } + threads: { + description: "The number of threads to use for alignment.", + category: "advanced" + } + sortThreads: { + description: "The number of threads to use for sorting.", + 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 chose not to address.", + category: "advanced" + } + + outputBam: "The produced BAM file." + outputBamIndex: "The index of the produced BAM file." + } } struct BwaIndex {