diff --git a/survivor.wdl b/survivor.wdl new file mode 100644 index 0000000000000000000000000000000000000000..f4fdc4b1dae4ee6a267887903581180f3798e848 --- /dev/null +++ b/survivor.wdl @@ -0,0 +1,42 @@ +version 1.0 + +import "common.wdl" + +task Merge { + input{ + Array[File] filePaths + Int breakpointDistance = 1000 + Int suppVecs = 2 + Int svType = 1 + Int strandType = 1 + Int distanceBySvSize = 0 + Int minSize = 30 + String sample + String outputPath + Int memory = 128 + } + + command <<< + set -e + mkdir -p $(dirname ~{outputPath}) + echo '~{sep="\n" filePaths}' > fileList + SURVIVOR merge \ + fileList \ + ~{breakpointDistance} \ + ~{suppVecs} \ + ~{svType} \ + ~{strandType} \ + ~{distanceBySvSize} \ + ~{minSize} \ + ~{outputPath} + >>> + + output { + File mergedVcf = "~{outputPath}" + } + + runtime { + docker: "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0" + memory: memory + } +}