diff --git a/bwa.wdl b/bwa.wdl index 05c8716af2ea03b1ca1e1127f1df3ed48104e02a..b0b1daf753377237c4d7f333ab6feee57b79b034 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -42,6 +42,21 @@ task Mem { memory: memory docker: dockerImage } + + parameter_meta { + read1: {description: "The first or single end fastq file.", category: "required"} + read2: {description: "The second end fastq file.", category: "common"} + bwaIndex: {description: "The BWA index files.", category: "required"} + outputPath: {description: "The location the output BAM file should be written to.", category: "required"} + readgroup: {description: "The readgroup to be assigned to the reads. See BWA mem's `-R` option.", category: "common"} + + threads: {description: "The number of threads to use.", category: "advanced"} + memory: {description: "The amount of memory this job will use.", category: "advanced"} + picardXmx: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.", + 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 Kit { @@ -91,47 +106,20 @@ task Kit { } 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 choose not to address.", - category: "advanced" - } + # inputs + 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 choose not to address.", + category: "advanced"} + # outputs outputBam: "The produced BAM file." outputBamIndex: "The index of the produced BAM file." }