diff --git a/chunked-scatter.wdl b/chunked-scatter.wdl new file mode 100644 index 0000000000000000000000000000000000000000..97affd289fc338f8eb7bacb4c78576c8e48c259b --- /dev/null +++ b/chunked-scatter.wdl @@ -0,0 +1,33 @@ +version 1.0 + +task ChunkedScatter { + input { + File inputFile + String prefix = "./scatter" + Int? chunkSize + Int? overlap + Int? minimumBasesPerFile + + String dockerImage = "alpine:latest" #TODO + } + + command { + set -e + mkdir -p ~{prefix} + chunked-scatter \ + -p ~{prefix} \ + -i ~{inputFile} \ + ~{"-c " + chunkSize} \ + ~{"-o " + overlap} \ + ~{"-m " + minimumBasesPerFile} + } + + output { + Array[File] scatters = glob(prefix + "_*.bed") + } + + runtime { + memory: 4 + docker: dockerImage + } +} \ No newline at end of file