diff --git a/bowtie.wdl b/bowtie.wdl index 72a396412d5f6edb9546adf1b946067be5031667..18fd6146adb6ea1b606f9d7b3bec6753d2c8fca4 100644 --- a/bowtie.wdl +++ b/bowtie.wdl @@ -80,6 +80,27 @@ task Bowtie { memory: memory docker: dockerImage } + + parameter_meta { + readsUpstream: {description: "The first-/single-end fastq files.", category: "required"} + readsDownstream: {description: "The second-end fastq files.", category: "common"} + outputPath: {description: "The location the output BAM file should be written to.", category: "common"} + indexFiles: {description: "The index files for bowtie.", category: "required"} + seedmms: {description: "Equivalent to bowtie's `--seedmms` option.", category: "advanced"} + seedlen: {description: "Equivalent to bowtie's `--seedlen` option.", category: "advanced"} + k: {description: "Equivalent to bowtie's `-k` option.", category: "advanced"} + best: {description: "Equivalent to bowtie's `--best` flag.", category: "advanced"} + strata: {description: "Equivalent to bowtie's `--strata` flag.", category: "advanced"} + allowContain: {description: "Equivalent to bowtie's `--allow-contain` flag.", category: "advanced"} + samRG: {description: "Equivalent to bowtie's `--sam-RG` option.", category: "advanced"} + + picardXmx: {description: "The maximum memory available to the picard (used for sorting the output). Should be lower than `memory` to accommodate JVM overhead and bowtie's memory usage.", + category: "advanced"} + threads: {description: "The number of threads to use.", 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"} + } } struct BowtieIndex {